scripts/selectSNV.R

In belleau/simAnc: What the Package Does (One Line, Title Case)

#!/usr/bin/env Rscript
argv = commandArgs(trailingOnly=TRUE)

library(devtools)
load_all(path = "/mnt/wigclust18/data/unsafe/belleau/beatHaplo/subsetMix/packages/simAnc")

sampleRef <- argv[1]
nbSim <- as.numeric(argv[2])
minFreq <- as.numeric(argv[3])

nameSel <- gsub(".rds", "", sampleRef)


PATH_1K <- "/mnt/wigclust5/data/unsafe/belleau/process1000G/samples1000gUnrelated/"
for(c in seq_len(22)){
    chr <- paste0("chr", c)
    PATH_OUT <- paste0("data/simRes.", nameSel, ".", nbSim,"/", chr, "/")

    fileMatFreq <- paste0(PATH_1K, "genotypeSample/", chr, "/matFreqSNV", chr,".txt.bz2")
    matFreq <- read.csv2(fileMatFreq, header=FALSE)
    colnames(matFreq) <- c("chr", "pos", "ref", "alt", "AF", "EAS_AF" ,"EUR_AF", "AFR_AF", "AMR_AF", "SAS_AF")

    infoSNV <- parseSelMinFreq(snv=matFreq, minFreq)

    saveRDS(infoSNV, paste0(PATH_OUT, "infoSNV.f", minFreq,".rds"))
}

q()