getReadCountsFromBAM: Calculation of read counts from BAM files.

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

Calculation of read counts from BAM files.

Description

Generates the read counts from BAM Files. 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

getReadCountsFromBAM(BAMFiles, sampleNames, refSeqNames, WL = 25000,
  parallel = 0, ...)

Arguments

BAMFiles	BAMFiles
sampleNames	The corresponding sample names to the BAM Files.
refSeqNames	Names of the reference sequence that should be analyzed. The name must appear in the header of the BAM file. If it is not given the function will select the first reference sequence that appears in the header of the BAM files. Can be set to analyze multipe chromosomes at once, e.g. refSeqNames=c("chr1","chr2")
WL	Windowlength. Length of the initial segmentation of the genome in basepairs. Should be chosen such that on the average 100 reads are contained in each segment.
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.

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)
bamDataRanges <- getReadCountsFromBAM(BAMFiles,
					sampleNames=paste("Sample",1:3),WL=5000)
X <- getReadCountsFromBAM(BAMFiles,
					sampleNames=paste("Sample",1:3),WL=5000,parallel=2)

gpovysil/cn.mops documentation built on Feb. 4, 2024, 10:18 a.m.