===Plink - Part 1 - Data QC===
plink --file GWAS
plink --file GWAS --mind 0.10 --recode --out GWAS_clean_mind
plink --file GWAS_clean3 --het
###### in R
Dataset <- read.table("plink.het", header=TRUE, sep="", na.strings="NA", dec=".", strip.white=TRUE) mean(Dataset$F) sd(Dataset$F) jpeg("hist.jpeg", height=1000, width=1000) hist(scale(Dataset$F), xlim=c(-4,4)) dev.off() q() ###### plink --file GWAS_clean3 --pheno pheno.txt --pheno-name Aff --hardy ##### in R hardy = read.table("plink.hwe", header = T) names(hardy) hwe_prob = hardy[which(hardy$P < 0.0000009),] hwe_prob q() ########## plink --file GWAS_clean3 --exclude HWE_out.txt --recode --out GWAS_clean4
===Plink - Part 2 - Controlling for Substructure===
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plink --file GWAS_clean4 --genome --cluster --mds-plot 10
#### in R
gws_adjusted = aff_C1C2[which(aff_C1C2$P < 0.0000001),]
gws_adjusted
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