Day2 Maize

source("./R/EigenGWAS_Friends.R")
#demo
FN="./demo/mHapMap3"
PC=5
inbred=T
RunEigenGWAS(FN, PC, inbred, "./demo/gear.jar")

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

EigenValuePlot(FN, 5)

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)