fmsURL <- "http://www.stat-gen.org/book.e1/data/FMS_data.txt"
fms <- read.delim(file=fmsURL, header=T, sep="\t")
attach(fms)
data.frame(id, actn3_r577x, actn3_rs540874, actn3_rs1815739, actn3_1671064, Term, Gender, Age, Race, NDRM.CH,DRM.CH)[1:20,]
## id actn3_r577x actn3_rs540874 actn3_rs1815739 actn3_1671064 Term
## 1 FA-1801 CC GG CC AA 02-1
## 2 FA-1802 CT GA TC GA 02-1
## 3 FA-1803 CT GA TC GA 02-1
## 4 FA-1804 CT GA TC GA 02-1
## 5 FA-1805 CC GG CC AA 02-1
## 6 FA-1806 CT GA TC GA 02-1
## 7 FA-1807 TT AA TT GG 02-1
## 8 FA-1808 CT GA TC GA <NA>
## 9 FA-1809 CT GA TC GA 02-1
## 10 FA-1810 CC GG CC AA 02-1
## 11 FA-1811 CC GG CC AA <NA>
## 12 FA-1812 CT GA TC GA 02-1
## 13 FA-1813 CT GA TC GA 02-1
## 14 FA-1814 CT GA TC GA 02-1
## 15 FA-1815 <NA> <NA> <NA> <NA> <NA>
## 16 FA-1816 TT GA TC GA 02-1
## 17 FA-1817 CT GA TC GA <NA>
## 18 FA-1818 CT GA TC GA <NA>
## 19 FA-1819 CT GG CC AA 02-3
## 20 FA-1820 CC GA TC GA 02-3
## Gender Age Race NDRM.CH DRM.CH
## 1 Female 27 Caucasian 40.0 40.0
## 2 Male 36 Caucasian 25.0 0.0
## 3 Female 24 Caucasian 40.0 0.0
## 4 Female 40 Caucasian 125.0 0.0
## 5 Female 32 Caucasian 40.0 20.0
## 6 Female 24 Hispanic 75.0 0.0
## 7 Female 30 Caucasian 100.0 0.0
## 8 <NA> NA <NA> NA NA
## 9 Female 28 Caucasian 57.1 -14.3
## 10 Male 27 Hispanic 33.3 0.0
## 11 <NA> NA <NA> NA NA
## 12 Female 30 Caucasian 20.0 0.0
## 13 Female 20 Caucasian 25.0 25.0
## 14 Female 23 African Am 100.0 25.0
## 15 <NA> NA <NA> NA NA
## 16 Female 24 Caucasian 28.6 12.5
## 17 <NA> NA <NA> NA NA
## 18 <NA> NA <NA> NA NA
## 19 Male 34 Caucasian 7.1 -7.1
## 20 Female 31 Caucasian 75.0 20.0
#Identifying the minor allele and its frequency
attach(fms)
## The following objects are masked from fms (pos = 3):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
GenoCount <- summary(actn3_rs540874)
GenoCount
## AA GA GG NA's
## 226 595 395 181
NumbObs <- sum(!is.na(actn3_rs540874))
GenoFreq <- as.vector(GenoCount/NumbObs)
GenoFreq
## [1] 0.1858553 0.4893092 0.3248355 0.1488487
FreqA <- (2*GenoFreq[1] + GenoFreq[2])/2
FreqA
## [1] 0.4305099
FreqG <- (GenoFreq[2] + 2*GenoFreq[3])/2
FreqG
## [1] 0.5694901
library(genetics)
## Loading required package: combinat
##
## Attaching package: 'combinat'
## The following object is masked from 'package:utils':
##
## combn
## Loading required package: gdata
## gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
##
## gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
##
## Attaching package: 'gdata'
## The following object is masked from 'package:stats':
##
## nobs
## The following object is masked from 'package:utils':
##
## object.size
## The following object is masked from 'package:base':
##
## startsWith
## Loading required package: gtools
## Loading required package: MASS
## Loading required package: mvtnorm
##
## NOTE: THIS PACKAGE IS NOW OBSOLETE.
##
## The R-Genetics project has developed an set of enhanced genetics
## packages to replace 'genetics'. Please visit the project homepage
## at http://rgenetics.org for informtion.
##
##
## Attaching package: 'genetics'
## The following objects are masked from 'package:base':
##
## %in%, as.factor, order
Geno <- genotype(actn3_rs540874,sep="")
summary(Geno)
##
## Number of samples typed: 1216 (87%)
##
## Allele Frequency: (2 alleles)
## Count Proportion
## G 1385 0.57
## A 1047 0.43
## NA 362 NA
##
##
## Genotype Frequency:
## Count Proportion
## G/G 395 0.32
## G/A 595 0.49
## A/A 226 0.19
## NA 181 NA
##
## Heterozygosity (Hu) = 0.4905439
## Poly. Inf. Content = 0.3701245
hgdpURL <- "http://www.stat-gen.org/book.e1/data/HGDP_AKT1.txt"
hgdp <- read.delim(file=hgdpURL, header=T, sep="\t")
virco <- read.csv(file="Virco_data.csv", header=T, sep=",")
#Chi-squared test for association
attach(fms)
## The following objects are masked from fms (pos = 9):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 10):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
NamesEsr1Snps <- names(fms)[substr(names(fms),1,4)=="esr1"]
NamesEsr1Snps
## [1] "esr1_rs1801132" "esr1_rs1042717" "esr1_rs2228480" "esr1_rs2077647"
## [5] "esr1_rs9340799" "esr1_rs2234693"
fmsEsr1 <- fms[,is.element(names(fms),NamesEsr1Snps)]
Trait <- as.numeric(pre.BMI>25)
newFunction <- function(Geno){
ObsTab <- table(Trait,Geno)
return(chisq.test(ObsTab)$p.value)
}
apply(fmsEsr1,2,newFunction)
## esr1_rs1801132 esr1_rs1042717 esr1_rs2228480 esr1_rs2077647 esr1_rs9340799
## 0.4440720 0.0264659 0.1849870 0.1802880 0.1606800
## esr1_rs2234693
## 0.1675418
Geno <- fmsEsr1[,2]
ObsTab <- table(Trait,Geno)
ObsTab
## Geno
## Trait AA GA GG
## 0 30 246 380
## 1 30 130 184
#Fisher's exact test for association
newFunction <- function(Geno){
ObsTab <- table(Trait,Geno)
return(fisher.test(ObsTab)$p.value)
}
apply(fmsEsr1,2,newFunction)
## esr1_rs1801132 esr1_rs1042717 esr1_rs2228480 esr1_rs2077647 esr1_rs9340799
## 0.46053113 0.02940733 0.18684765 0.17622428 0.15896064
## esr1_rs2234693
## 0.16945636
#Cochran-Armitage (C-A) trend test for association
library(coin)
## Loading required package: survival
attach(fms)
## The following objects are masked from fms (pos = 5):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 12):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 13):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
Geno <- esr1_rs1042717
Trait <- as.numeric(pre.BMI>25)
GenoOrd <- ordered(Geno)
independence_test(Trait~GenoOrd,teststat="quad", scores=list(GenoOrd=c(0,1,2)))
##
## Asymptotic General Independence Test
##
## data: Trait by GenoOrd (AA < GA < GG)
## chi-squared = 4.4921, df = 1, p-value = 0.03405
#Two-sample tests of association for a quantitative trait
attach(fms)
## The following objects are masked from fms (pos = 3):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 6):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 13):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 14):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
NamesResistinSnps <- names(fms)[substr(names(fms),1,8)=="resistin"]
fmsResistin <- fms[,is.element(names(fms),NamesResistinSnps)]
library(genetics)
TtestPval <- function(Geno){
alleleMajor <- allele.names(genotype(Geno, sep="",
reorder="freq"))[1]
GenoWt <- paste(alleleMajor, alleleMajor, sep="")
GenoBin <- as.numeric(Geno!=GenoWt)[!is.na(Geno)]
Trait <- NDRM.CH[!is.na(Geno)]
return(t.test(Trait[GenoBin==1], Trait[GenoBin==0])$p.value)
}
apply(fmsResistin,2,TtestPval)
## resistin_c30t resistin_c398t resistin_g540a resistin_c980g resistin_c180g
## 0.04401614 0.08098567 0.11578470 0.27828906 0.03969448
## resistin_a537c
## 0.06573061
Geno <- fms$"resistin_c180g"
table(Geno)
## Geno
## CC CG GG
## 330 320 89
GenoWt <- names(table(Geno))[table(Geno)==max(table(Geno))]
GenoWt
## [1] "CC"
GenoBin <- as.numeric(Geno!=GenoWt)[!is.na(Geno)]
Trait <- NDRM.CH[!is.na(Geno)]
t.test(Trait[GenoBin==1],Trait[GenoBin==0])
##
## Welch Two Sample t-test
##
## data: Trait[GenoBin == 1] and Trait[GenoBin == 0]
## t = -2.0618, df = 552.16, p-value = 0.03969
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -10.9729548 -0.2658088
## sample estimates:
## mean of x mean of y
## 50.43503 56.05441
#M-sample tests of association for a quantitative trait
attach(fms)
## The following objects are masked from fms (pos = 3):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 4):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 7):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 14):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 15):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
Geno <- as.factor(resistin_c180g)
Trait <- NDRM.CH
AnovaMod <- lm(Trait~Geno, na.action=na.exclude)
summary(AnovaMod)
##
## Call:
## lm(formula = Trait ~ Geno, na.action = na.exclude)
##
## Residuals:
## Min 1Q Median 3Q Max
## -56.054 -22.754 -6.054 15.346 193.946
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 56.054 2.004 27.973 <2e-16 ***
## GenoCG -5.918 2.864 -2.067 0.0392 *
## GenoGG -4.553 4.356 -1.045 0.2964
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 33.05 on 603 degrees of freedom
## (791 observations deleted due to missingness)
## Multiple R-squared: 0.007296, Adjusted R-squared: 0.004003
## F-statistic: 2.216 on 2 and 603 DF, p-value: 0.11
kruskal.test(Trait, Geno, na.action=na.exclude)
##
## Kruskal-Wallis rank sum test
##
## data: Trait and Geno
## Kruskal-Wallis chi-squared = 4.9268, df = 2, p-value = 0.08515
#Linear regression
attach(fms)
## The following objects are masked from fms (pos = 3):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 4):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 5):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 8):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 15):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 16):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
Geno <- actn3_r577x
Trait <- NDRM.CH
ModFull <- lm(Trait~Geno+Gender+Geno*Gender, na.action=na.exclude)
summary(ModFull)
##
## Call:
## lm(formula = Trait ~ Geno + Gender + Geno * Gender, na.action = na.exclude)
##
## Residuals:
## Min 1Q Median 3Q Max
## -68.778 -20.258 -4.351 14.970 184.970
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 53.558 2.964 18.068 < 2e-16 ***
## GenoCT 11.471 3.882 2.955 0.003251 **
## GenoTT 15.219 4.286 3.551 0.000414 ***
## GenderMale -13.507 4.769 -2.832 0.004777 **
## GenoCT:GenderMale -14.251 6.117 -2.330 0.020160 *
## GenoTT:GenderMale -13.537 6.867 -1.971 0.049153 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 30.8 on 597 degrees of freedom
## (794 observations deleted due to missingness)
## Multiple R-squared: 0.1423, Adjusted R-squared: 0.1351
## F-statistic: 19.81 on 5 and 597 DF, p-value: < 2.2e-16
ModReduced <- lm(Trait~Geno+Gender, na.action=na.exclude)
anova(ModReduced, ModFull)
## Analysis of Variance Table
##
## Model 1: Trait ~ Geno + Gender
## Model 2: Trait ~ Geno + Gender + Geno * Gender
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 599 572345
## 2 597 566518 2 5826.8 3.0702 0.04715 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
NewDat <- data.frame(Geno=rep(c("CC","CT","TT"),2),
Gender=c(rep("Female",3), rep("Male",3)))
predict.lm(ModFull, NewDat, interval="prediction", level=0.95)
## fit lwr upr
## 1 53.55833 -7.220257 114.33692
## 2 65.02980 4.330657 125.72895
## 3 68.77778 7.973847 129.58171
## 4 40.05147 -20.890899 100.99384
## 5 37.27168 -23.494571 98.03793
## 6 41.73437 -19.235589 102.70434
#Measuring LD using D0
library(genetics)
attach(fms)
## The following objects are masked from fms (pos = 3):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 4):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 5):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 6):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 9):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 16):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 17):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
actn3_r577x[1:10]
## [1] CC CT CT CT CC CT TT CT CT CC
## Levels: CC CT TT
actn3_rs540874[1:10]
## [1] GG GA GA GA GG GA AA GA GA GG
## Levels: AA GA GG
Actn3Snp1 <- genotype(actn3_r577x,sep="")
Actn3Snp2 <- genotype(actn3_rs540874,sep="")
Actn3Snp1[1:10]
## [1] "C/C" "C/T" "C/T" "C/T" "C/C" "C/T" "T/T" "C/T" "C/T" "C/C"
## Alleles: C T
class(Actn3Snp1)
## [1] "genotype" "factor"
Esr1Snp1 <- genotype(esr1_rs1801132,sep="")
LD(Actn3Snp1,Esr1Snp1)$"D'"
## [1] 0.1122922
#Measuring pairwise LD for a group of SNPs
Actn3Snp3 <- genotype(actn3_rs1815739,sep="")
Actn3Snp4 <- genotype(actn3_1671064,sep="")
Actn3AllSnps <- data.frame(Actn3Snp1,Actn3Snp2,Actn3Snp3,Actn3Snp4)
LD(Actn3AllSnps)$"D'"
## Actn3Snp1 Actn3Snp2 Actn3Snp3 Actn3Snp4
## Actn3Snp1 NA 0.8858385 0.9266828 0.8932708
## Actn3Snp2 NA NA 0.9737162 0.9556019
## Actn3Snp3 NA NA NA 0.9575870
## Actn3Snp4 NA NA NA NA
library(LDheatmap)
## Loading required package: grid
LDheatmap(Actn3AllSnps, LDmeasure="D'")
#Measuring LD based on r2 and the chi squared statistic
attach(fms)
## The following objects are masked from fms (pos = 5):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 6):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 7):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 8):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 9):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 12):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 19):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 20):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
library(genetics)
Actn3Snp1 <- genotype(actn3_r577x,sep="")
Actn3Snp2 <- genotype(actn3_rs540874,sep="")
LD(Actn3Snp1,Actn3Snp2)$"R^2"
## [1] 0.6179236
LD(Actn3Snp1,Actn3Snp2)
##
## Pairwise LD
## -----------
## D D' Corr
## Estimates: 0.1945726 0.8858385 0.7860811
##
## X^2 P-value N
## LD Test: 895.9891 0 725
#Determining average LD across multiple SNPs
LDMat <- LD(Actn3AllSnps)$"D'"
mean(LDMat,na.rm=T)
## [1] 0.9321162
#Population substructure and LD
ObsCount <- matrix(c(136,64,64,136),2)
ObsCount
## [,1] [,2]
## [1,] 136 64
## [2,] 64 136
ExpCount <- chisq.test(ObsCount)$expected
ExpCount
## [,1] [,2]
## [1,] 100 100
## [2,] 100 100
#Testing for HWE using Pearson's chi squared test
attach(hgdp)
## The following object is masked from fms (pos = 3):
##
## Gender
## The following object is masked from fms (pos = 6):
##
## Gender
## The following object is masked from fms (pos = 7):
##
## Gender
## The following object is masked from fms (pos = 8):
##
## Gender
## The following object is masked from fms (pos = 9):
##
## Gender
## The following object is masked from fms (pos = 10):
##
## Gender
## The following object is masked from fms (pos = 13):
##
## Gender
## The following object is masked from fms (pos = 20):
##
## Gender
## The following object is masked from fms (pos = 21):
##
## Gender
Akt1Snp1 <- AKT1.C0756A
ObsCount <- table(Akt1Snp1)
Nobs <- sum(ObsCount)
ObsCount
## Akt1Snp1
## AA CA CC
## 48 291 724
FreqC <- (2 * ObsCount[3] + ObsCount[2])/(2*Nobs)
ExpCount <- c(Nobs*(1-FreqC)^2, 2*Nobs*FreqC*(1-FreqC),Nobs*FreqC^2)
ExpCount
## CC CC CC
## 35.22319 316.55362 711.22319
ChiSqStat <- sum((ObsCount - ExpCount)^2/ExpCount)
ChiSqStat
## [1] 6.926975
qchisq(1-0.05,df=1)
## [1] 3.841459
library(genetics)
Akt1Snp1 <- genotype(AKT1.C0756A, sep="")
HWE.chisq(Akt1Snp1)
##
## Pearson's Chi-squared test with simulated p-value (based on 10000
## replicates)
##
## data: tab
## X-squared = 6.927, df = NA, p-value = 0.009899
#Testing for HWE using Fisher's exact test
attach(hgdp)
## The following objects are masked from hgdp (pos = 3):
##
## AKT1.C0756A, AKT1.C6024T, AKT1.G2347T, AKT1.G2375A, Gender,
## Geographic.area, Geographic.origin, ID, Population, Well
## The following object is masked from fms (pos = 4):
##
## Gender
## The following object is masked from fms (pos = 7):
##
## Gender
## The following object is masked from fms (pos = 8):
##
## Gender
## The following object is masked from fms (pos = 9):
##
## Gender
## The following object is masked from fms (pos = 10):
##
## Gender
## The following object is masked from fms (pos = 11):
##
## Gender
## The following object is masked from fms (pos = 14):
##
## Gender
## The following object is masked from fms (pos = 21):
##
## Gender
## The following object is masked from fms (pos = 22):
##
## Gender
Akt1Snp1Maya <- AKT1.C0756A[Population=="Maya"]
ObsCount <- table(Akt1Snp1Maya)
ObsCount
## Akt1Snp1Maya
## AA CA CC
## 1 6 18
Nobs <- sum(ObsCount)
FreqC <- (2 * ObsCount[3] + ObsCount[2])/(2*Nobs)
ExpCount <- c(Nobs*(1-FreqC)^2, 2*Nobs*FreqC*(1-FreqC),Nobs*FreqC^2)
ExpCount
## CC CC CC
## 0.64 6.72 17.64
n11 <- ObsCount[3]
n12 <- ObsCount[2]
n22 <- ObsCount[1]
n1 <- 2*n11+n12
Num <- 2^n12 * factorial(Nobs)/prod(factorial(ObsCount))
Denom <- factorial(2*Nobs) / (factorial(n1)*factorial(2*Nobs-n1))
FisherP1 <- Num/Denom
FisherP1
## CA
## 0.4011216
library(genetics)
Akt1Snp1Maya <- genotype(AKT1.C0756A[Population=="Maya"], sep="")
HWE.exact(Akt1Snp1Maya)
##
## Exact Test for Hardy-Weinberg Equilibrium
##
## data: Akt1Snp1Maya
## N11 = 18, N12 = 6, N22 = 1, N1 = 42, N2 = 8, p-value = 0.4843
ObsDat <- matrix(c(160,80,80,80),2)
chisq.test(ObsDat,correct=FALSE)
##
## Pearson's Chi-squared test
##
## data: ObsDat
## X-squared = 11.111, df = 1, p-value = 0.0008581
#HWE and geographic origin
attach(hgdp)
## The following objects are masked from hgdp (pos = 3):
##
## AKT1.C0756A, AKT1.C6024T, AKT1.G2347T, AKT1.G2375A, Gender,
## Geographic.area, Geographic.origin, ID, Population, Well
## The following objects are masked from hgdp (pos = 4):
##
## AKT1.C0756A, AKT1.C6024T, AKT1.G2347T, AKT1.G2375A, Gender,
## Geographic.area, Geographic.origin, ID, Population, Well
## The following object is masked from fms (pos = 5):
##
## Gender
## The following object is masked from fms (pos = 8):
##
## Gender
## The following object is masked from fms (pos = 9):
##
## Gender
## The following object is masked from fms (pos = 10):
##
## Gender
## The following object is masked from fms (pos = 11):
##
## Gender
## The following object is masked from fms (pos = 12):
##
## Gender
## The following object is masked from fms (pos = 15):
##
## Gender
## The following object is masked from fms (pos = 22):
##
## Gender
## The following object is masked from fms (pos = 23):
##
## Gender
table(Geographic.area)
## Geographic.area
## Central Africa Central America China Israel
## 119 50 184 148
## Japan New Guinea Northern Africa Northern Europe
## 31 17 30 16
## Pakistan Russia South Africa South America
## 200 67 8 58
## Southeast Asia Southern Europe
## 11 125
library(genetics)
Akt1Snp1 <- genotype(AKT1.C0756A, sep="")
HWEGeoArea <- tapply(Akt1Snp1,INDEX=Geographic.area,HWE.chisq)
HWEGeoArea$"Central Africa"
##
## Pearson's Chi-squared test with simulated p-value (based on 10000
## replicates)
##
## data: tab
## X-squared = 0.23224, df = NA, p-value = 0.672
HWEGeoArea$"South America"
##
## Pearson's Chi-squared test with simulated p-value (based on 10000
## replicates)
##
## data: tab
## X-squared = 27.239, df = NA, p-value = 9.999e-05
#Generating a similarity matrix
attach(fms)
## The following object is masked from hgdp (pos = 3):
##
## Gender
## The following object is masked from hgdp (pos = 4):
##
## Gender
## The following object is masked from hgdp (pos = 5):
##
## Gender
## The following objects are masked from fms (pos = 6):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 9):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 10):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 11):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 12):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 13):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 16):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 23):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
## The following objects are masked from fms (pos = 24):
##
## acdc_rs1501299, ace_id, actn3_1671064, actn3_r577x,
## actn3_rs1815739, actn3_rs540874, adrb2_1042713, adrb2_1042714,
## adrb2_rs1042718, adrb3_4994, Age, agrp_5030980, akt1_a15756t,
## akt1_a22889g, akt1_a7699g, akt1_c10744t_c12886t, akt1_c15676t,
## akt1_c5854t_c7996t, akt1_c6024t_c8166t, akt1_c6148t_c8290t,
## akt1_c832g_c3359g, akt1_c9756a_c11898t, akt1_g14803t,
## akt1_g15129a, akt1_g1780a_g363a, akt1_g20703a, akt1_g22187a,
## akt1_g23477a, akt1_g2347t_g205t, akt1_g2375a_g233a,
## akt1_g288c, akt1_g4362c, akt1_t10598a_t12740a,
## akt1_t10726c_t12868c, akt1_t22932c, akt1_t8407g, akt2_2304186,
## akt2_7254617, akt2_969531, akt2_rs892118, ampd1_c34t,
## ankrd6_a545t, ankrd6_a550t, ankrd6_g197805a, ankrd6_i128l,
## ankrd6_k710x, ankrd6_m485l, ankrd6_p636l, ankrd6_q122e,
## ankrd6_t233m, apoe_c472t, ardb1_1801253, b2b, bcl6_1056932,
## bcl6_17797517, bcl6_3774298, bcl6_4686467, bmp2_235768,
## bmp2_rs15705, c8orf68_rs6983944, Calc.post.BMI,
## carp.exon3_snp3, carp_3utr, carp_a8470g, carp_c105t,
## carp_exon3_snp1, carp_exon3_snp2, carp_exon5_snp1,
## carp_exon5_snp2, carp_exon6_ag, carp_exon8_ct, cast_rs754615,
## cast_rs7724759, cav2_q130e, Center, CHOL, CHOL_HDL_C,
## CK_day_0, CK_day_2, CK_day_4, cntf_g6a, cox5b_11904110,
## cox5b_17022045, CRP, ctsf_572846, D_Post_B_VOL, D_Post_BM_VOL,
## D_Post_F_VOL, D_Post_M_VOL, D_Post_WA_VOL, D_Post_WM_VOL,
## D_Pre_B_VOL, D_Pre_BM_VOL, D_Pre_F_VOL, D_Pre_M_VOL,
## D_Pre_WA_VOL, D_Pre_WM_VOL, D23.CH, D23_DIFF, DBP,
## ddit_rs1053227, Dom.Arm, DRM.CH, DRM_DIFF, esr1_rs1042717,
## esr1_rs1801132, esr1_rs2077647, esr1_rs2228480,
## esr1_rs2234693, esr1_rs9340799, esr2_1256112, esr2_3020450,
## fatso, fbox32_rs2891770, fbox32_rs3739287, fbox32_rs4871385,
## fbox32_rs6690663, fbox32_rs6983944, FINS, FLGU, fst_1423560,
## fst_722910, fstl1_rs9631455, galntl1_rs8005903, gapd_7307229,
## gapd_7971637, gdf8_1225t, gdf8_e164k, gdf8_k153r, gdf8_p198a,
## gdf8_rs1805085, gdf8_rs1805086, gdf8_t55a, Gender,
## gnb3_rs5443, gs_s287nga, HDL_C, HOMA, hsd11b1_rs3753519,
## hsd11b1_rs4844880, hsd11b1_rs846907, hsd11b1_rs846909,
## hsd11b1_rs846910, hsd11b1_rs846911, hsd11b1_rs860185, id,
## igf1_2288377, igf1_pro, igf1_t1245c, igf2_2230949,
## igf2_3213216, igf2_3213220, igf2_3213221, igf2_rs680,
## igfbp3_2132570, igfbp3_6670, il15_1057972, il15_1589241,
## il15_rs2296135, il15ra_2228059, il15ra_3136618, il6_c174g,
## il6_g572c, insig2_rs7566605, irs1_g972r, kchj11_rs5219, LDL_C,
## lep_2167270, lepr_1137100, lepr_1137101, lepr_1805096,
## lepr_8179183, lrp5_snp2, lrp5_snp3, lrp5_snp4, Mean_BP,
## Met_syn, mgst3_4147542, mgst3_7549530, mlck_c37885a,
## mlck_c49t, mlck_g91689t, mulk_3757470, mylk_c37885a,
## mylk_g91689t, myod1_rs2249104, ND_Post_B_VOL, ND_Post_BM_VOL,
## ND_Post_F_VOL, ND_Post_M_VOL, ND_Post_WA_VOL, ND_Post_WM_VOL,
## ND_Pre_B_VOL, ND_Pre_BM_VOL, ND_Pre_F_VOL, ND_Pre_M_VOL,
## ND_Pre_WA_VOL, ND_Pre_WM_VOL, ND23.CH, ND23_DIFF, NDRM.CH,
## NDRM_DIFF, nnmt_g5082t, nos3_rs1799983, nr3c1_rs10482614,
## nr3c1_rs10482616, nr3c1_rs4582314, nr3c1_rs4634384,
## nr3c1_rs6195, opg_2073618, opg_3102735, p2rx2_6560891,
## p2rx2_7966242, p2ry2_2511241, p2ry2_rs1783596, pai1_4g5g,
## pcr13_snp1, pcr15_snp1, pcr15_snp2, pcr15_snp3, pcr15_snp4,
## pcr5_snp1, pcr5_snp2, pcr8_snp1, pgc1_g76039a, pgm1_2284998,
## pik3_rs3173908, pik3cg_4727666, Post.Height, Post.weight,
## Post_D_avg, Post_DRM_Max, Post_LBi_Avg, Post_LTri_Avg,
## Post_ND_avg, Post_NDRM_Max, Post_RBi_Avg, Post_RTri_Avg,
## Post1_D_AVG, Post1_D1, Post1_D2, Post1_D3, Post1_ND_AVG,
## Post1_ND1, Post1_ND2, Post1_ND3, Post2_D_AVG, Post2_D1,
## Post2_D2, Post2_D3, Post2_ND_AVG, Post2_ND1, Post2_ND2,
## Post2_ND3, ppar_gp12a, ppara_135539, ppara_1800206,
## ppara_4252778, pparg_c1a_rs8192678, prdx6_4382766, pre.BMI,
## Pre.height, Pre.HR, Pre.weight, Pre_DRM_Max, Pre_LBi_Avg,
## Pre_LTri_Avg, Pre_NDRM_Max, Pre_RBi_Avg, Pre_RTri_Avg,
## pygm_620006, Race, rankl_17458177, rankl_17536280,
## rankl_17639305, rankl_4531631, resistin_a537c, resistin_c180g,
## resistin_c30t, resistin_c398t, resistin_c980g, resistin_g540a,
## rnf28_c16242t, rs11630261, rs302964, rs849409, runx_12526462,
## SBP, slc35f1_rs10484290, slc35f1_rs12110370, Status,
## syngr2_c886t, tcfl72_12255372, tcfl72_7903146,
## tcfl72_rs12255372, tcfl72_rs7903146, tdp52l1_9321028, Term,
## TG, tnfa_g308a, tnni1_2799672, tnni1_3738287, tpd52l1_3778458,
## tpd52l1_3799736, tpd52l1_4896782, tpd52l1_514096, ucp2_ct,
## V1_D_AVG, V1_D1, V1_D2, V1_D3, V1_ND_AVG, V1_ND1, V1_ND2,
## V1_ND3, V123_D_AVG, V123_ND_AVG, V2_D_AVG, V2_D1, V2_D2,
## V2_D3, V2_ND_AVG, V2_ND1, V2_ND2, V2_ND3, V23_D_AVG,
## V23_ND_AVG, V3_D_AVG, V3_D1, V3_D2, V3_D3, V3_ND_AVG, V3_ND1,
## V3_ND2, V3_ND3, vdr_bsm1, vdr_fok1, vdr_rs731236, vdr_taq1,
## vim_6602186, visfatin_10487820, visfatin_10953502,
## visfatin_2041681, visfatin_3801272, visfatin_6947766,
## visfatin_929604, VLDL_TG
NamesAkt1Snps <- names(fms)[substr(names(fms),1,4)=="akt1"]
NamesAkt1Snps
## [1] "akt1_t22932c" "akt1_g15129a" "akt1_g14803t"
## [4] "akt1_c10744t_c12886t" "akt1_t10726c_t12868c" "akt1_t10598a_t12740a"
## [7] "akt1_c9756a_c11898t" "akt1_t8407g" "akt1_a7699g"
## [10] "akt1_c6148t_c8290t" "akt1_c6024t_c8166t" "akt1_c5854t_c7996t"
## [13] "akt1_c832g_c3359g" "akt1_g288c" "akt1_g1780a_g363a"
## [16] "akt1_g2347t_g205t" "akt1_g2375a_g233a" "akt1_g4362c"
## [19] "akt1_c15676t" "akt1_a15756t" "akt1_g20703a"
## [22] "akt1_g22187a" "akt1_a22889g" "akt1_g23477a"
FMSgeno <- fms[,is.element(names(fms),NamesAkt1Snps)]
FMSgenoNum <- data.matrix(FMSgeno)
FMSgenoNum[is.na(FMSgenoNum)] <- 4
DistFmsGeno <- as.matrix(dist(FMSgenoNum))
DistFmsGeno[1:5,1:5]
## 1 2 3 4 5
## 1 0.000000 4.795832 5.291503 3.741657 3.162278
## 2 4.795832 0.000000 2.236068 3.872983 3.000000
## 3 5.291503 2.236068 0.000000 3.162278 3.741657
## 4 3.741657 3.872983 3.162278 0.000000 2.449490
## 5 3.162278 3.000000 3.741657 2.449490 0.000000
#Multidimensional scaling (MDS) for identifying population substructure
plot(cmdscale(DistFmsGeno),xlab="C1",ylab="C2")
abline(v=0,lty=2)
abline(h=4,lty=2)
#Principal components analysis (PCA) for identifying population substructure
PCFMS <- prcomp(FMSgenoNum)
plot(PCFMS$"x"[,1],PCFMS$"x"[,2],xlab="PC1",ylab="PC2")
