EigenGWAS_Friends.R

Table of contents

1 Setup

source("./R/EigenGWAS_Friends.R")
#demo
FN="./demo/arab"
PC=5
inbred=T
RunEigenGWAS(FN, PC, inbred, "./demo/gear.jar")

2 PCA

####GRM stats
layout(matrix(1:2, 1, 2))
grmStats(FN)

EigenValuePlot(FN, PC)

layout(matrix(1:6, 2, 3, byrow = T))
for(i in 1:PC) {
  dat=read.table(paste0(FN, ".", i, ".egwas"), as.is = T, header = T)
  dat$P=dat$PGC
  manhattan(dat,bty='l',cex=0.5, pch=16)
}

3 Plot for each eigenvector

miamiPlot(FN, 1, Log1 = T, Log2 = F, cex=0.5, pch=16, bty="l")

EigenGWASPlot(FN, 1)

miamiPlot(FN, 2, Log1 = TRUE, Log2 = F, cex=0.5, pch=16, bty="l")

EigenGWASPlot(FN, 2)

miamiPlot(FN, 3, Log1 = TRUE, Log2 = F, cex=0.5, pch=16, bty="l")

EigenGWASPlot(FN, 3)

miamiPlot(FN, 4, Log1 = TRUE, Log2 = F, cex=0.5, pch=16, bty="l")

EigenGWASPlot(FN, 4)

miamiPlot(FN, 5, Log1 = TRUE, Log2 = F, cex=0.5, pch=16, bty="l")

EigenGWASPlot(FN, 5)