getReadCountsFromBAM: Calculation of read counts from BAM files.

Description Usage Arguments Value Author(s) Examples

View source: R/getReadCountsFromBAM.R

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

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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. 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 klambauer@bioinf.jku.at

Examples

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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)

cn.mops documentation built on May 31, 2017, 11:52 a.m.