8.16 GWAS of all SNPs with PLINK

Now let’s allow PLINK to run the statistical tests for all SNPs by removing the --snp flag.

system(command = "./plink --file genotypes --linear --allow-no-sex --pheno GS451_IC50.txt --pheno-name GS451_IC50")

The plink.assoc.linear file should now have ~260,000 lines. Load the file into R to look at the results:

results <- read.table(file = "plink.assoc.linear",
                      header = TRUE) %>%
  # order table by lowest pvalue
  arrange(P)

head(results)

##   CHR        SNP       BP A1 TEST NMISS   BETA   STAT         P
## 1  19  rs7257475 20372113  T  ADD    88 -3.008 -6.876 9.311e-10
## 2  19 rs10413538 20370690  T  ADD    86 -3.026 -6.805 1.395e-09
## 3  21  rs2826383 20844081  A  ADD   166  3.031  5.866 2.392e-08
## 4  19 rs12972967 20358400  T  ADD    89 -2.421 -5.939 5.760e-08
## 5   2  rs1358578 51626897  A  ADD   166  2.111  5.307 3.571e-07
## 6  17  rs3094508 33137048  C  ADD    89  3.532  5.230 1.156e-06