getSegmentReadCountsFromBAM: Calculation of read counts from BAM files for predefined...

In cn.mops: cn.mops - Mixture of Poissons for CNV detection in NGS data

Description

Generates the read counts from BAM Files for predefined segments. This is the appropiate choice for exome sequencing data, where the bait regions, target regions or exons are the predefined segments. These counts are necessary for CNV detection methods based on depth of coverage information.

This function can also be run in a parallel version.

Usage

getSegmentReadCountsFromBAM(BAMFiles, GR, sampleNames, parallel = 0, ...)

Arguments

BAMFiles	BAMFiles
GR	A genomic ranges object that contains the genomic coordinates of the segments.
sampleNames	The corresponding sample names to the BAM Files.
parallel	The number of parallel processes to be used for this function. Default=0.
...	Additional parameters passed to the function "countBamInGRanges" of the Bioconductor package "exomeCopy". Quality filters for read counts can be adjusted there. Please see "??countBamInGRanges" for more information.

Value

An instance of "GRanges", that contains the breakpoints of the initial segments and the raw read counts that were extracted from the BAM files. This object can be used as input for cn.mops and other CNV detection methods.

Author(s)

Guenter Klambauer [e-mail]

Examples

BAMFiles <- list.files(system.file("extdata", package="cn.mops"),pattern=".bam$", full.names=TRUE)
gr <- GRanges(c("20","20"),IRanges(c(60000,70000),c(70000,80000)))
bamDataRanges <- getSegmentReadCountsFromBAM(BAMFiles,GR=gr)
bamDataRanges <- getSegmentReadCountsFromBAM(BAMFiles,GR=gr,parallel=2)

cn.mops documentation built on Nov. 8, 2020, 5:59 p.m.