Changes

==Plink - Part 1 - Data QC== 

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$F), xlim=c(Plink -4,4)) dev.off() q() ###### plink Part 2 --file GWAS_clean3 --pheno pheno.txt --pheno-name Aff --hardy ##### in R hardy Controlling for Substructure= read.table("plink.hwe", header = T) names(hardy) hwe_prob = hardy[which(hardy$P < 0.0000009),] hwe_prob q() ########## plink --file GWAS_clean3 --exclude HWE_out.txt --recode --out GWAS_clean4

===Plink Part 2 - Controlling for Substructure=== plink --file GWAS_clean4 --genome --cluster --mds-plot 10

mydata$pch[mydata$Group==1 ] <-15 mydata$pch[mydata$Group==2 ] <-16 mydata$pch[mydata$Group==3 ] <-2 jpeg("mds.jpeg", height=500, width=500) plot(mydata$C1, mydata$C2 ,pch=mydata$pch) dev.off() q() ###### plink --file GWAS_clean4 --pheno pheno.txt --pheno-name Aff --logistic --adjust --out unadj plink --file GWAS_clean4 --genome --cluster --pca 10 header plink --file GWAS_clean4 --pheno pheno.txt --pheno-name Aff --covar plink.eigenvec --covar-name PC1 --logistic --adjust --out PC1 plink --file GWAS_clean4 --pheno pheno.txt --pheno-name Aff --covar plink.eigenvec --covar-name PC1-PC2 --logistic --adjust --out PC1-PC2 #### in R broadqq <-function(pvals, title) { observed <- sort(pvals) observed¶ lobs <- -(log10(observed)) expected <- c(1:length(observed)) ¶ lexp <- -(log10(expected / (length(expected)+1))) plot(c(0,7), c(0,7), col="red", lwd=3, type="l", xlab="Expected (-logP)", ylab="Observed (-logP)", xlim=c(0,max(lobs)), ylim=c(0,max(lobs)), las=1, xaxs="i", yaxs="i", bty="l", main = title) points(lexp, lobs, pch=23, cex=.4, bg="black") }