qnormall:

In dvera/arthur: What the package does (short line)

Usage

qnormall(seqfiles, arrayfiles, cores = "max")

Arguments

seqfiles
arrayfiles
cores

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (seqfiles, arrayfiles, cores = "max") 
{
    library(parallel)
    if (cores == "max") {
        cores = detectCores() - 1
    }
    numseqfiles = length(seqfiles)
    numarrayfiles = length(arrayfiles)
    arrayheads <- lapply(1:numarrayfiles, function(x) read.delim(pipe(paste("head", 
        arrayfiles[x]))))
    numarraycells <- unlist(lapply(arrayheads, ncol)) - 2
    cat("pooling all data\n")
    allscores <- unlist(mclapply(1:(numarrayfiles + numseqfiles), 
        function(x) {
            if (x <= numseqfiles) {
                cat("loading", seqfiles[x], "\n")
                as.numeric(readLines(pipe(paste("cut -f 4", seqfiles[x]))))
            }
            else {
                a = x - numseqfiles
                cat("loading", arrayfiles[a], "\n")
                d <- unlist(read.delim(pipe(paste("cut -f", paste(3:numarraycells[a], 
                  collapse = ","), arrayfiles[a]))))
                d <- as.numeric(d[2:length(d)])
                return(d)
            }
        }, mc.cores = cores))
    if (cores > numseqfiles) {
        cores2 = numseqfiles
    }
    else {
        cores2 = cores
    }
    cat("normalizing sequencing data\n")
    mclapply(1:numseqfiles, function(x) {
        seqdata <- read.tsv(seqfiles[x])
        curref <- sample(allscores, nrow(seqdata))
        seqdata[, 4][order(seqdata[, 4])] <- curref[order(curref)]
        outname <- paste(basename(removeext(seqfiles[x])), "_qnormToPool.bg", 
            sep = "")
        print(outname)
        write.tsv(seqdata, file = outname)
    }, mc.cores = cores2)
    if (cores > numarrayfiles) {
        cores2 = numarrayfiles
    }
    else {
        cores2 = cores
    }
    cat("normalizing array data\n")
    mclapply(1:numarrayfiles, function(x) {
        for (i in 1:numarraycells[x]) {
            arraydata <- read.delim(pipe(paste("cut -f 1,2,", 
                i + 2, " ", arrayfiles[x], sep = "")), header = TRUE)
            curref <- sample(allscores, nrow(arraydata))
            arraydata[, 3][order(arraydata[, 3])] <- curref[order(curref)]
            outname <- paste(basename(removeext(arrayfiles[x])), 
                "_", colnames(arraydata)[3], "_qnormToPool.txt", 
                sep = "")
            print(outname)
            write.tsv(arraydata, file = outname)
        }
    }, mc.cores = cores2)
  }

dvera/arthur documentation built on June 5, 2019, 5:12 a.m.