taskBedsPlinkOut = function(hub, taskName, plinkOutFile, pvalThresh=5e-2, nMinShift=1, nMaxShift) {
hubtask = hub[[taskName]]
hubtask$pvalThresh = pvalThresh
hubtask$nMinShift = nMinShift
hubtask$nMaxShift = nMaxShift
checkFileExists(plinkOutFile)
message(sprintf("Reading p values from plink result file: %s", plinkOutFile))
pvalDat = readplinkoutr(plinkOutFile, c("SNP", "P"))
message(sprintf("Extracting SNPs based on P values, threshold: %f...", pvalThresh))
hubtask$extractSnpVector = pvalDat$SNP[which(pvalDat$P < pvalThresh)]
hubtask$extractSnpFile = paste( hubtask$bedStem, "_extract_by_p_", format(pvalThresh, scientific=TRUE), ".snplist", sep="")
write.table(hubtask$extractSnpVector, file=hubtask$extractSnpFile, quote=FALSE, row.names=FALSE, col.names=FALSE)
## suppressWarnings({
## file.remove(c(hubtask$taskBedPath, hubtask$taskBimPath, hubtask$taskFamPath))
## file.remove(c(hubtask$taskShiftFilesBed, hubtask$taskShiftFilesBim, hubtask$taskShiftFilesFam))
## })
tmplist = list()
tmplist$bfile = hub$bedStem
tmplist$out = hubtask$bedStem
tmplist$extract = hubtask$extractSnpFile
tmplist$make_bed = ""
message("Generating new plink files based on extracted SNPs...")
do.call(plinkr, tmplist)
tmphub = collrinfo(wDir=hubtask$taskPath)
bedcollinfo(tmphub, TRUE, hubtask$nMinShift, hubtask$nMaxShift)
suppressWarnings(appendEnv(hubtask, tmphub))
invisible(NULL)
}
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