# Clear workspace
rm(list = ls())
# Set working directory
setwd("J:/Sungjin_Pig_Data/Sungjin_Pig_Data_analysis")
# load data files
#Phenotype file
phenotypes <- read.table("Pheno.txt")
colnames(phenotypes) <- c("ARN","SSIRE", "TBATCH", "RBATCH","SEX","PAR", "MPAR",
"TAGE","BWT","ADGW","ADGP","BF2","D90kg","BF1","BF3",
"BFM","DP","EMA","NBA","LWT","ABW","WEI","TNB","HNB",
"SBP","LSD","RFI")
# Remove all records with BWT ==0
require(dplyr)
## Loading required package: dplyr
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
dat01 <- filter(phenotypes,BWT > 0)
#Without TNB
formula2 <- BWT~SEX + MPAR
model2 <- lm(formula=formula2, data=phenotypes)
summary(model2)
##
## Call:
## lm(formula = formula2, data = phenotypes)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.7664 -0.3868 0.1030 0.4452 1.6503
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.51260 0.01799 28.49 <2e-16 ***
## SEX 0.44731 0.01206 37.09 <2e-16 ***
## MPAR 0.19490 0.00316 61.68 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.5786 on 10064 degrees of freedom
## Multiple R-squared: 0.377, Adjusted R-squared: 0.3769
## F-statistic: 3045 on 2 and 10064 DF, p-value: < 2.2e-16
#With TNB
formula1 <- BWT ~ SEX + MPAR + TNB
model1 <- lm(formula=formula1, data=phenotypes)
summary(model1)
##
## Call:
## lm(formula = formula1, data = phenotypes)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.34971 -0.28347 -0.05906 0.23872 2.33368
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.254111 0.017088 73.39 <2e-16 ***
## SEX 0.202224 0.010025 20.17 <2e-16 ***
## MPAR 0.102726 0.002760 37.22 <2e-16 ***
## TNB -0.106624 0.001367 -78.02 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.4568 on 10063 degrees of freedom
## Multiple R-squared: 0.6118, Adjusted R-squared: 0.6117
## F-statistic: 5287 on 3 and 10063 DF, p-value: < 2.2e-16
#With service ssire
formula3 <- BWT ~ SEX + MPAR + TNB + SSIRE
model3 <- lm(formula=formula3, data=phenotypes)
summary(model3)
##
## Call:
## lm(formula = formula3, data = phenotypes)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.23351 -0.28595 -0.02117 0.22639 2.16839
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.340243 0.016605 80.715 < 2e-16 ***
## SEX 0.177174 0.009623 18.411 < 2e-16 ***
## MPAR 0.089512 0.002669 33.533 < 2e-16 ***
## TNB -0.033180 0.004037 -8.220 2.29e-16 ***
## SSIREDD16004111 -0.332126 0.106605 -3.115 0.001842 **
## SSIREDD16027016 -0.868004 0.095443 -9.095 < 2e-16 ***
## SSIREDD16060077 -0.132094 0.151132 -0.874 0.382125
## SSIREDD16060181 -0.546215 0.083368 -6.552 5.96e-11 ***
## SSIREDD16062110 -0.624600 0.082941 -7.531 5.49e-14 ***
## SSIREDD16063049 -0.645990 0.100582 -6.423 1.40e-10 ***
## SSIREDD16065016 -0.435548 0.082249 -5.295 1.21e-07 ***
## SSIREDD16066161 -0.491864 0.149599 -3.288 0.001013 **
## SSIREDD16069047 -0.546873 0.142604 -3.835 0.000126 ***
## SSIREDD16071095 -0.747998 0.118992 -6.286 3.39e-10 ***
## SSIREDD16075097 -0.799850 0.119345 -6.702 2.17e-11 ***
## SSIREDD16076170 -0.731677 0.078514 -9.319 < 2e-16 ***
## SSIREDD17001098 -0.629097 0.097472 -6.454 1.14e-10 ***
## SSIREDD17002084 -1.008329 0.098983 -10.187 < 2e-16 ***
## SSIREDD17004057 -0.660002 0.084756 -7.787 7.54e-15 ***
## SSIREDD17013013 -0.263983 0.220798 -1.196 0.231885
## SSIREDD17019078 -0.856211 0.132026 -6.485 9.28e-11 ***
## SSIREDD17033140 -0.476542 0.081827 -5.824 5.93e-09 ***
## SSIREDD17034130 -0.763078 0.076433 -9.984 < 2e-16 ***
## SSIREDD17037015 -1.351518 0.252522 -5.352 8.89e-08 ***
## SSIREDD17041036 -0.857389 0.083153 -10.311 < 2e-16 ***
## SSIREDD17043039 -0.952681 0.152336 -6.254 4.17e-10 ***
## SSIREDD17100076 -0.639938 0.101063 -6.332 2.52e-10 ***
## SSIREDD17110038 -0.838858 0.088883 -9.438 < 2e-16 ***
## SSIREDD17111182 -1.001139 0.109849 -9.114 < 2e-16 ***
## SSIREDD17114015 -1.229859 0.254118 -4.840 1.32e-06 ***
## SSIREDD17117078 -0.918775 0.100295 -9.161 < 2e-16 ***
## SSIREDD17118025 -0.247163 0.168511 -1.467 0.142477
## SSIREDD17132039 -0.867508 0.087547 -9.909 < 2e-16 ***
## SSIREDD18004161 -0.630138 0.102286 -6.161 7.53e-10 ***
## SSIREDD18005055 -0.856152 0.097045 -8.822 < 2e-16 ***
## SSIREDD18006046 -0.643392 0.181693 -3.541 0.000400 ***
## SSIREDD18010056 -0.679675 0.092595 -7.340 2.30e-13 ***
## SSIREDD18010096 -0.568292 0.255514 -2.224 0.026163 *
## SSIREDD18021047 -0.604380 0.096688 -6.251 4.25e-10 ***
## SSIREDD18033098 -0.648807 0.123461 -5.255 1.51e-07 ***
## SSIREDD18034131 -0.790645 0.107574 -7.350 2.14e-13 ***
## SSIREDD18036121 -1.139167 0.145504 -7.829 5.41e-15 ***
## SSIREDD18038045 -0.871653 0.125195 -6.962 3.56e-12 ***
## SSIREDD18039024 -0.760640 0.091193 -8.341 < 2e-16 ***
## SSIREDD18044048 -0.732332 0.131501 -5.569 2.63e-08 ***
## SSIREDD18062049 -0.774739 0.087910 -8.813 < 2e-16 ***
## SSIREDD18066063 -1.015774 0.126877 -8.006 1.32e-15 ***
## SSIREDD18090016 -0.608976 0.101900 -5.976 2.36e-09 ***
## SSIREDD18090064 -0.487944 0.079624 -6.128 9.23e-10 ***
## SSIREDD18101035 -0.130605 0.311649 -0.419 0.675167
## SSIREDD18102096 -0.941138 0.121251 -7.762 9.19e-15 ***
## SSIREDD18105018 -0.762986 0.086621 -8.808 < 2e-16 ***
## SSIREDD18106076 -1.258614 0.197574 -6.370 1.97e-10 ***
## SSIREDD18111016 -0.715230 0.106609 -6.709 2.07e-11 ***
## SSIREDD18113012 -0.799733 0.083222 -9.610 < 2e-16 ***
## SSIREDD18131094 -1.041378 0.127757 -8.151 4.04e-16 ***
## SSIREDD18133016 -0.893883 0.099486 -8.985 < 2e-16 ***
## SSIREDD18136069 -0.541721 0.158902 -3.409 0.000654 ***
## SSIREDD19002018 -0.660033 0.114134 -5.783 7.56e-09 ***
## SSIREDD19010079 -0.741123 0.084840 -8.736 < 2e-16 ***
## SSIREDD19011048 -0.846041 0.159919 -5.290 1.25e-07 ***
## SSIREDD19036172 -0.780723 0.094629 -8.250 < 2e-16 ***
## SSIREDD19037170 -0.407865 0.094084 -4.335 1.47e-05 ***
## SSIREDD19040076 -1.106961 0.094221 -11.749 < 2e-16 ***
## SSIREDD19062074 -1.119260 0.223321 -5.012 5.48e-07 ***
## SSIREDD19067075 -0.475703 0.182211 -2.611 0.009048 **
## SSIREDD19069171 -0.839694 0.127164 -6.603 4.23e-11 ***
## SSIREDD19090048 -0.669068 0.138978 -4.814 1.50e-06 ***
## SSIREDD19092079 -0.606925 0.200123 -3.033 0.002430 **
## SSIREDD19130042 -1.210504 0.221193 -5.473 4.54e-08 ***
## SSIREHYPOR6725C -1.115913 0.080099 -13.932 < 2e-16 ***
## SSIREHYPOR6750C -1.207739 0.118955 -10.153 < 2e-16 ***
## SSIREHYPOR6810C -1.206660 0.078327 -15.405 < 2e-16 ***
## SSIREHYPOR6818C -1.089527 0.090934 -11.981 < 2e-16 ***
## SSIREHYPOR6845C -1.209319 0.077464 -15.611 < 2e-16 ***
## SSIREHYPOR6879C -1.185619 0.089618 -13.230 < 2e-16 ***
## SSIREHYPOR7440C -1.188635 0.086180 -13.793 < 2e-16 ***
## SSIREHYPOR7448C -0.885806 0.109009 -8.126 4.96e-16 ***
## SSIREHYPOR7460C -0.985537 0.096384 -10.225 < 2e-16 ***
## SSIREHYPOR7467C -1.120953 0.103194 -10.863 < 2e-16 ***
## SSIREHYPOR7481C -1.041282 0.095548 -10.898 < 2e-16 ***
## SSIREHYPOR7501C -0.891652 0.096816 -9.210 < 2e-16 ***
## SSIREHYPOR7613C -1.177324 0.116833 -10.077 < 2e-16 ***
## SSIREHYPOR7638C -1.048176 0.121694 -8.613 < 2e-16 ***
## SSIREHYPOR7648C -0.932956 0.080209 -11.632 < 2e-16 ***
## SSIREHYPOR7670C -1.101754 0.111165 -9.911 < 2e-16 ***
## SSIREHYPOR7690C -1.221564 0.096342 -12.679 < 2e-16 ***
## SSIREHYPOR7694C -1.216587 0.118621 -10.256 < 2e-16 ***
## SSIREHYPOR7702C -1.098291 0.092023 -11.935 < 2e-16 ***
## SSIREHYPOR7753C -1.146237 0.087991 -13.027 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.4357 on 9977 degrees of freedom
## Multiple R-squared: 0.6498, Adjusted R-squared: 0.6467
## F-statistic: 208 on 89 and 9977 DF, p-value: < 2.2e-16
#make a breed variable
BREED <- substr(phenotypes$ARN,1,2)
phenotypes2 <-cbind(phenotypes,BREED)
#With breed variable
formula4 <- BWT ~ SEX + MPAR + TNB + SSIRE # + TBATCH #BREED +D90kg
model4 <- lm(formula=formula4, data=phenotypes2)
summary(model4)
##
## Call:
## lm(formula = formula4, data = phenotypes2)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.23351 -0.28595 -0.02117 0.22639 2.16839
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.340243 0.016605 80.715 < 2e-16 ***
## SEX 0.177174 0.009623 18.411 < 2e-16 ***
## MPAR 0.089512 0.002669 33.533 < 2e-16 ***
## TNB -0.033180 0.004037 -8.220 2.29e-16 ***
## SSIREDD16004111 -0.332126 0.106605 -3.115 0.001842 **
## SSIREDD16027016 -0.868004 0.095443 -9.095 < 2e-16 ***
## SSIREDD16060077 -0.132094 0.151132 -0.874 0.382125
## SSIREDD16060181 -0.546215 0.083368 -6.552 5.96e-11 ***
## SSIREDD16062110 -0.624600 0.082941 -7.531 5.49e-14 ***
## SSIREDD16063049 -0.645990 0.100582 -6.423 1.40e-10 ***
## SSIREDD16065016 -0.435548 0.082249 -5.295 1.21e-07 ***
## SSIREDD16066161 -0.491864 0.149599 -3.288 0.001013 **
## SSIREDD16069047 -0.546873 0.142604 -3.835 0.000126 ***
## SSIREDD16071095 -0.747998 0.118992 -6.286 3.39e-10 ***
## SSIREDD16075097 -0.799850 0.119345 -6.702 2.17e-11 ***
## SSIREDD16076170 -0.731677 0.078514 -9.319 < 2e-16 ***
## SSIREDD17001098 -0.629097 0.097472 -6.454 1.14e-10 ***
## SSIREDD17002084 -1.008329 0.098983 -10.187 < 2e-16 ***
## SSIREDD17004057 -0.660002 0.084756 -7.787 7.54e-15 ***
## SSIREDD17013013 -0.263983 0.220798 -1.196 0.231885
## SSIREDD17019078 -0.856211 0.132026 -6.485 9.28e-11 ***
## SSIREDD17033140 -0.476542 0.081827 -5.824 5.93e-09 ***
## SSIREDD17034130 -0.763078 0.076433 -9.984 < 2e-16 ***
## SSIREDD17037015 -1.351518 0.252522 -5.352 8.89e-08 ***
## SSIREDD17041036 -0.857389 0.083153 -10.311 < 2e-16 ***
## SSIREDD17043039 -0.952681 0.152336 -6.254 4.17e-10 ***
## SSIREDD17100076 -0.639938 0.101063 -6.332 2.52e-10 ***
## SSIREDD17110038 -0.838858 0.088883 -9.438 < 2e-16 ***
## SSIREDD17111182 -1.001139 0.109849 -9.114 < 2e-16 ***
## SSIREDD17114015 -1.229859 0.254118 -4.840 1.32e-06 ***
## SSIREDD17117078 -0.918775 0.100295 -9.161 < 2e-16 ***
## SSIREDD17118025 -0.247163 0.168511 -1.467 0.142477
## SSIREDD17132039 -0.867508 0.087547 -9.909 < 2e-16 ***
## SSIREDD18004161 -0.630138 0.102286 -6.161 7.53e-10 ***
## SSIREDD18005055 -0.856152 0.097045 -8.822 < 2e-16 ***
## SSIREDD18006046 -0.643392 0.181693 -3.541 0.000400 ***
## SSIREDD18010056 -0.679675 0.092595 -7.340 2.30e-13 ***
## SSIREDD18010096 -0.568292 0.255514 -2.224 0.026163 *
## SSIREDD18021047 -0.604380 0.096688 -6.251 4.25e-10 ***
## SSIREDD18033098 -0.648807 0.123461 -5.255 1.51e-07 ***
## SSIREDD18034131 -0.790645 0.107574 -7.350 2.14e-13 ***
## SSIREDD18036121 -1.139167 0.145504 -7.829 5.41e-15 ***
## SSIREDD18038045 -0.871653 0.125195 -6.962 3.56e-12 ***
## SSIREDD18039024 -0.760640 0.091193 -8.341 < 2e-16 ***
## SSIREDD18044048 -0.732332 0.131501 -5.569 2.63e-08 ***
## SSIREDD18062049 -0.774739 0.087910 -8.813 < 2e-16 ***
## SSIREDD18066063 -1.015774 0.126877 -8.006 1.32e-15 ***
## SSIREDD18090016 -0.608976 0.101900 -5.976 2.36e-09 ***
## SSIREDD18090064 -0.487944 0.079624 -6.128 9.23e-10 ***
## SSIREDD18101035 -0.130605 0.311649 -0.419 0.675167
## SSIREDD18102096 -0.941138 0.121251 -7.762 9.19e-15 ***
## SSIREDD18105018 -0.762986 0.086621 -8.808 < 2e-16 ***
## SSIREDD18106076 -1.258614 0.197574 -6.370 1.97e-10 ***
## SSIREDD18111016 -0.715230 0.106609 -6.709 2.07e-11 ***
## SSIREDD18113012 -0.799733 0.083222 -9.610 < 2e-16 ***
## SSIREDD18131094 -1.041378 0.127757 -8.151 4.04e-16 ***
## SSIREDD18133016 -0.893883 0.099486 -8.985 < 2e-16 ***
## SSIREDD18136069 -0.541721 0.158902 -3.409 0.000654 ***
## SSIREDD19002018 -0.660033 0.114134 -5.783 7.56e-09 ***
## SSIREDD19010079 -0.741123 0.084840 -8.736 < 2e-16 ***
## SSIREDD19011048 -0.846041 0.159919 -5.290 1.25e-07 ***
## SSIREDD19036172 -0.780723 0.094629 -8.250 < 2e-16 ***
## SSIREDD19037170 -0.407865 0.094084 -4.335 1.47e-05 ***
## SSIREDD19040076 -1.106961 0.094221 -11.749 < 2e-16 ***
## SSIREDD19062074 -1.119260 0.223321 -5.012 5.48e-07 ***
## SSIREDD19067075 -0.475703 0.182211 -2.611 0.009048 **
## SSIREDD19069171 -0.839694 0.127164 -6.603 4.23e-11 ***
## SSIREDD19090048 -0.669068 0.138978 -4.814 1.50e-06 ***
## SSIREDD19092079 -0.606925 0.200123 -3.033 0.002430 **
## SSIREDD19130042 -1.210504 0.221193 -5.473 4.54e-08 ***
## SSIREHYPOR6725C -1.115913 0.080099 -13.932 < 2e-16 ***
## SSIREHYPOR6750C -1.207739 0.118955 -10.153 < 2e-16 ***
## SSIREHYPOR6810C -1.206660 0.078327 -15.405 < 2e-16 ***
## SSIREHYPOR6818C -1.089527 0.090934 -11.981 < 2e-16 ***
## SSIREHYPOR6845C -1.209319 0.077464 -15.611 < 2e-16 ***
## SSIREHYPOR6879C -1.185619 0.089618 -13.230 < 2e-16 ***
## SSIREHYPOR7440C -1.188635 0.086180 -13.793 < 2e-16 ***
## SSIREHYPOR7448C -0.885806 0.109009 -8.126 4.96e-16 ***
## SSIREHYPOR7460C -0.985537 0.096384 -10.225 < 2e-16 ***
## SSIREHYPOR7467C -1.120953 0.103194 -10.863 < 2e-16 ***
## SSIREHYPOR7481C -1.041282 0.095548 -10.898 < 2e-16 ***
## SSIREHYPOR7501C -0.891652 0.096816 -9.210 < 2e-16 ***
## SSIREHYPOR7613C -1.177324 0.116833 -10.077 < 2e-16 ***
## SSIREHYPOR7638C -1.048176 0.121694 -8.613 < 2e-16 ***
## SSIREHYPOR7648C -0.932956 0.080209 -11.632 < 2e-16 ***
## SSIREHYPOR7670C -1.101754 0.111165 -9.911 < 2e-16 ***
## SSIREHYPOR7690C -1.221564 0.096342 -12.679 < 2e-16 ***
## SSIREHYPOR7694C -1.216587 0.118621 -10.256 < 2e-16 ***
## SSIREHYPOR7702C -1.098291 0.092023 -11.935 < 2e-16 ***
## SSIREHYPOR7753C -1.146237 0.087991 -13.027 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.4357 on 9977 degrees of freedom
## Multiple R-squared: 0.6498, Adjusted R-squared: 0.6467
## F-statistic: 208 on 89 and 9977 DF, p-value: < 2.2e-16
# Extract data
dat1 <- data.frame(phenotypes[c(1:9,23)])
write.table(dat1, file = "data_BWT.txt", sep = " ", col.names = FALSE, quote = FALSE)