convertBamToBigWig: Convert Bam files to BigWig Files using coverage on genome...

In TapscottLab/UCSCTrackTools: Tools to convert BAM files to BigWig and to create session track line

Usage

convertBamToBigWig(bamFiles, NH.weight = FALSE, output.dir = NULL,
                   cores=1L, singleEnded=TRUE)

Arguments

bamFiles	Vector of charactor strings of the bam files.
NH.weight	Logical indicating whether to weight the coverage by the NH tab.
output.dir	Character string indicating the location of the output bigWig files.
cores	The number of precessors to use.
singleEnded	Logical indicated whether the reads are single ended.

Value

List of coverage.

Author(s)

Chao-Jen Wong <[e-mail]>

Examples

## Not run: 
ngsDir <- "/shared/ngs/illumina/acampbel/150408_SN367_0511_BHJ33TADXX"
bamDir <- file.path(ngsDir, "tophat")

tmp <- list.files(file.path(bamDir, "bam"), pattern="\.bam$",
                  all.files=FALSE,
                  include.dirs=TRUE)
bamFiles <- file.path(bamDir, "bam", tmp)[1]

## convert Bam files to bw files
res <- UCSCTrackTools::convertBamToBigWig(bamFiles, NH.weight=FALSE)


## End(Not run)

TapscottLab/UCSCTrackTools documentation built on May 16, 2019, 2:28 a.m.