read2count: SAM/BAM/BED file reader helper for the metaseqr2 pipeline

In pmoulos/metaseqR2: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

SAM/BAM/BED file reader helper for the metaseqr2 pipeline

Description

This function is a helper for the metaseqr2 pipeline, for reading SAM/BAM or BED files when a read counts file is not available. It can also be used very easily in an autonomous manner.

Usage

    read2count(targets, annotation, fileType = targets$type,
        transLevel = "gene", utrOpts = list(frac = 1, 
        minLength = 300, downstream = 50), interFeature = FALSE, 
        rc = NULL)

Arguments

targets	a named list, the output of readTargets or an existing file with targets. See also the main metaseqr2 man page.
annotation	a GenomicRanges or data.frame with genomic coordinates to use for read counting. See also getAnnotation.
fileType	the type of raw input files. It can be "bed" for BED files or "sam", "bam" for SAM/BAM files. See the same argument in the main metaseqr2 function for the case of auto-guessing.
transLevel	see the transLevel argument in the main metaseqr2 function.
utrOpts	a named list with members frac which is the fraction (0-1) of the 3' UTR region to count reads in, minLength the minimum acceptable 3'UTR length irrespective of frac and downstream the number of base pairs to flank the end of the 3' UTR of transcripts when analyzing Quant-Seq data.
interFeature	see the inter.feature argument in summarizeOverlaps.
rc	the fraction of the available cores to use in a multicore system.

Value

A data frame with counts for each sample, ready to be passed to the main metaseqr2 pipeline.

Author(s)

Panagiotis Moulos

Examples

dataPath <- system.file("extdata",package="metaseqR2")
targets <- data.frame(samplename=c("C","T"),
    filename=file.path(dataPath,c("C.bam","T.bam")),  
    condition=c("Control","Treatment"),
    paired=c("single","single"),stranded=c("forward","forward"))
path <- tempdir()
write.table(targets,file=file.path(path,"targets.txt"),
    sep="\t",row.names=FALSE,quote=FALSE)
geneData <- loadAnnotation("mm10","ensembl","gene")
myTargets <- readTargets(file.path(path,"targets.txt"))
if (.Platform$OS.type == "unix") {
    r2c <- read2count(targets=myTargets,
        fileType=myTargets$type,annotation=geneData)
    geneCounts <- r2c$counts
    libsizeList <- r2c$libsize
}

pmoulos/metaseqR2 documentation built on May 20, 2024, 5:48 a.m.