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monogenea/3-poissonGWAS.R

Created October 7, 2019 18:48
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3-poissonGWAS.R
library(snpStats)
library(doParallel)
library(SNPRelate)
library(GenABEL)
library(dplyr)
source("GWASfunction.R")
load("PhenoGenoMap.RData")
# Use SNP call rate of 100%, MAF of 0.1 (very stringent)
maf <- 0.1
callRate <- 1
SNPstats <- col.summary(genData$SNP)
maf_call <- with(SNPstats, MAF > maf & Call.rate == callRate)
genData$SNP <- genData$SNP[,maf_call]
genData$MAP <- genData$MAP[maf_call,]
SNPstats <- SNPstats[maf_call,]
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