routine1 = function(wDir=".", taskName, plinkArgs, initGwas=FALSE, initGwasArgs, pFilter=.05, nMaxShift) {
setwd(wDir)
hubcollr = collrinfo()
bedcollinfo(hubcollr, genbed = FALSE)
taskinfo(hubcollr, taskName, plinkArgs, initGwasArgs, initGwas)
hubtask = hubcollr[[taskName]]
checkFileExists(hubtask$fullGwasOut)
taskBedsPlinkOut(hubcollr, taskName, hubtask$fullGwasOut, pFilter, 1, nMaxShift)
taskAnalyze(hubcollr, taskName)
readcoll.task(hubcollr, taskName)
contrastPlot(hubtask)
hubtask$taskContrastPlotFile = file.path(hubtask$taskPlotPath, "contrastPlot.png")
ggsave(plot = hubtask$contrastPlotOut, filename = hubtask$taskContrastPlotFile, width=10, height=5)
hubtask$workspaceImageFile = file.path(hubtask$taskPath, "taskWorkspace.RData")
save(hubcollr, file=hubtask$workspaceImageFile)
hubtask$contrastPlotOut
}
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