#' QCDH routine 1
#'
#' This routine collects info on the working directory, performs an
#' initial GWAS as a basis for SNP selection by p values, generates
#' bed files with collapsed genotypes, analyzes them, and saves intermediate
#' and final results in an environment named after the task.
#' This routine is called by \code{qcdhRoutine}.
#'
#' @param wDir Working directory. All paths within this function will be relative to this.
#' @param taskName Name of the QCDH task.
#' @param plinkArgs Arguments to be passed to PLINK (in QCDH analysis)
#' @param initGwas Whether to perform an initial GWAS
#' @param initGwasArgs Arguments to pass to PLINK for the initial GWAS
#' @param pFilter Filter out SNPs with p value higher than this (in the initial GWAS)
#' @param nMaxShift Maximum shift number (for genotype collapsing)
#' @param bpdiff Upper bound of distance between a pair of SNPs, default to 5e5
#' @return hubtask An environment containing info and results from the current task.
routine1 = function(wDir = ".", taskName, plinkArgs, initGwas=FALSE, initGwasArgs, pFilter=.05, nMaxShift, bpdiff = 5e5) {
setwd(wDir)
# collect info
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, bpdiff = bpdiff)
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
invisible(hubtask)
}
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