===GenABEL===
===GenABEL===
# Load files
library(GenABEL)
row.names(results(testb.qt))[results(testb.qt)$P1df < alpha]
results(testb.qt)$P1df[results(testb.qt)$P1df < alpha]
results(testb.qt)$Pc1df[results(testb.qt)$Pc1df < alpha]
===Plink - Part 1 - Data QC===
plink --file GWAS
plink --file GWAS --mind 0.10 --recode --out GWAS_clean_mind
q()
##########
plink --file GWAS_clean3 --exclude HWE_out.txt --recode --out GWAS_clean4 ===Plink - Part 2 - Controlling for Substructure===
plink --file GWAS_clean4 --genome --cluster --mds-plot 10
#### in R
broadqq <-function(pvals, title)
{
observed <- sort(pvals)
lobs <- -(log10(observed))