countBamListInGRanges: Get read counts for a list of BAM files and given count...

In bioinf-jku/panelcn.mops: CNV detection tool for targeted NGS panel data

Get read counts for a list of BAM files and given count windows

Description

Get read counts for a list of BAM files and given count windows

Usage

countBamListInGRanges(bam.files, countWindows, read.width = 150, ...)

Arguments

bam.files	list with absolute or relative paths to BAM files
countWindows	data.frame with contents of a BED file as returned by getWindows
read.width	read.width parameter for countBamInGRanges or FALSE if actual read width should be extracted from BAM file
...	additional parameters

Value

a GRanges object over the countWindows with read counts for each sample as elementMetadata

Examples

bed <- system.file("extdata/Genes_part.bed", package = "panelcn.mops")
countWindows <- getWindows(bed)
## Not run: 
testbam <- "SAMPLE1.bam"
test <- countBamListInGRanges(countWindows = countWindows,
                                bam.files = testbam, read.width = 150)

## End(Not run)

bioinf-jku/panelcn.mops documentation built on March 24, 2022, 1:19 a.m.