Below is a subset of results from the association of mQTLs and prostate cancer, showing only results for mQTLs associated with cg03227775 (a CpG in CARD11 associated observationally with shift work).
#setwd("C:/Users/ca16591/Dropbox/Bristol")
CARD11 <- read_delim("C:/Users/ca16591/Dropbox/Bristol/CARDL11.mQTLSNPs.csv","\t", escape_double = FALSE, trim_ws = TRUE)
dim(CARD11)
head(CARD11)
names(CARD11)
CARD11$BP <- CARD11$'SNP Pos'
# Obtain list of unique SNPs, taking just the first in the CARD11.
#new <- do.call(rbind, lapply(split(CARD11, CARD11$SNP), `[`, 1, ))
#dim(new)
#new$SNP
# Read in the results of the association between prostate cancer incidence and mQTLs
#setwd("Z:/data/protect/_devs/PROTECT_Clinical/data")
sorted_pca <- read_csv("Z:/data/protect/_devs/PROTECT_Clinical/data/sorted_pca_results06-02-2017.csv")
meQTL_list <- read.csv("Z:/data/protect/_devs/PROTECT_Clinical/data/meQTL_list.csv", sep="")
meQTL_list$BP <- meQTL_list$chromStart
BP_start <- sorted_pca[which(sorted_pca$BP %in% meQTL_list$BP),]
#mQTL_PCa_GWAS_results <- write.csv(BP_start, "BP_start.csv")
# Use base position (BP) to identify the set of CARD11-mQTL results in BP_start (the PRACTICAL mQTL and PCa analysis I did a few weeks ago)
CARD11_in_GWAS <- CARD11[which(CARD11$BP %in% BP_start$BP),]
# Subset BP_start by the list of CARD11-mqtl BP
CARD11_mQTL_results_in_PCa_mQTL_Analysis <- BP_start[which(BP_start$BP %in% CARD11_in_GWAS$BP),]
CARD11_mQTL_results_in_PCa_mQTL_Analysis
write.csv(CARD11_mQTL_results_in_PCa_mQTL_Analysis, "C:/Users/ca16591/Dropbox/Bristol/CARD11_mQTL_results_in_PCa_mQTL_Analysis.csv")
| 1 |
1459881 |
12 |
12:10945975:G:A |
10945975 |
G |
A |
0.7524 |
0.9655 |
1.0216 |
0.0121 |
0.07758 |
| 2 |
899003 |
7 |
rs1626708:2952886:C:T |
2952886 |
C |
T |
0.2692 |
0.8628 |
0.9890 |
0.0125 |
0.37480 |
| 3 |
899004 |
7 |
rs1182158:2954387:G:A |
2954387 |
G |
A |
0.2466 |
0.8937 |
0.9904 |
0.0126 |
0.44310 |
| 4 |
899002 |
7 |
rs1628709:2950020:C:T |
2950020 |
C |
T |
0.2418 |
0.8795 |
0.9904 |
0.0128 |
0.45280 |
| 5 |
899014 |
7 |
rs1636167:2972072:A:G |
2972072 |
A |
G |
0.2859 |
0.8666 |
0.9948 |
0.0122 |
0.66990 |
| 6 |
899012 |
7 |
rs1713909:2969508:G:A |
2969508 |
G |
A |
0.2328 |
0.9848 |
0.9968 |
0.0123 |
0.79670 |
| 7 |
899013 |
7 |
rs1621509 |
2969680 |
G |
A |
0.2288 |
0.9964 |
0.9973 |
0.0123 |
0.82570 |
| 8 |
899017 |
7 |
rs6945582:2976767:G:A |
2976767 |
G |
A |
0.1930 |
0.8072 |
1.0031 |
0.0145 |
0.83300 |
| 9 |
899005 |
7 |
rs1183080:2958504:G:A |
2958504 |
G |
A |
0.2522 |
0.9403 |
0.9983 |
0.0122 |
0.88940 |
| 10 |
899011 |
7 |
rs11773360:2968871:T:C |
2968871 |
T |
C |
0.2401 |
0.9724 |
0.9985 |
0.0122 |
0.89930 |
| 11 |
899007 |
7 |
rs17257217:2963120:C:T |
2963120 |
C |
T |
0.2501 |
0.9505 |
0.9985 |
0.0122 |
0.90430 |
| 12 |
899015 |
7 |
rs1713927:2973104:C:T |
2973104 |
C |
T |
0.1949 |
0.8718 |
0.9986 |
0.0139 |
0.91840 |
| 13 |
899009 |
7 |
rs1182137:2966138:G:A |
2966138 |
G |
A |
0.2484 |
0.9444 |
0.9989 |
0.0123 |
0.92640 |
| 14 |
899016 |
7 |
rs41404646:2974494:C:A |
2974494 |
C |
A |
0.1931 |
0.8434 |
0.9994 |
0.0142 |
0.96840 |
| 15 |
899008 |
7 |
rs1182139:2965269:C:T |
2965269 |
C |
T |
0.2417 |
0.9525 |
0.9995 |
0.0123 |
0.96940 |
| 16 |
899006 |
7 |
rs1636173:2962014:G:A |
2962014 |
G |
A |
0.2494 |
0.9479 |
1.0005 |
0.0122 |
0.96960 |
| 17 |
899010 |
7 |
rs1182135:2967688:C:T |
2967688 |
C |
T |
0.2434 |
0.9555 |
1.0000 |
0.0122 |
0.99980 |