Calculation of read counts from BAM files for predefined segments.

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. Note that the function is much faster, if the BAM files have an index file. The index file is assumed to be in the same folder and have an identical file name except that ".bai" is appended.

This function can also be run in a parallel version.

Usage

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getSegmentReadCountsFromBAM(BAMFiles, GR, sampleNames, mode, parallel = 0,
  BAIFiles = NULL)

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.

mode

Possible values are "paired" and "unpaired", whether the mapping algorithm was using a "paired" or "unpaired" strategy.

parallel

The number of parallel processes to be used for this function. Default=0.

BAIFiles

The names of the BAI files that belong to the BAM files. The vector has to be in the same order as the vector BAMFiles. If the BAI files have the same name as the BAM files, only with ".bai" attached, this parameter needs not be set. (Default = NULL).

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)
gr <- GRanges(c("20","20"),IRanges(c(60000,70000),c(70000,80000)))
bamDataRanges <- getSegmentReadCountsFromBAM(BAMFiles,GR=gr,mode="unpaired")
bamDataRanges <- getSegmentReadCountsFromBAM(BAMFiles,GR=gr,mode="unpaired",parallel=2)

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