ReadCountsFromBam: ReadCountsFromBam

In budczies/CNVPanelizer: Reliable CNV detection in targeted sequencing applications

Description

Returns a matrix with the read counts from a set of bam files.

Usage

ReadCountsFromBam(bamFilenames,
                sampleNames,
                gr,
                ampliconNames,
                minimumMappingQuality,
                removeDup = FALSE)

Arguments

bamFilenames	Vector of bamfile filepaths
sampleNames	Vector of sample names to be used as colums names instead of bam filepaths
gr	Genomic Range object as created by BedToGenomicRanges
ampliconNames	List of amplicon defining names
minimumMappingQuality	Minimum mapping quality
removeDup	Boolean value to remove duplicates. For reads with the same start site, end site and orientation only one is kept. For IonTorrent data this can be used to as an additional quality control. For Illumina data too many reads are being removed.

Value

A matrix with read counts where the rows represents the Amplicons and the columns represents the samples.

Author(s)

Thomas Wolf, Cristiano Oliveira

Examples

    
    
    
        ReadCountsFromBam(bamFilenames,
                            sampleNames,
                            gr,
                            ampliconNames,
                            removeDup)
    

budczies/CNVPanelizer documentation built on May 29, 2019, 1:41 p.m.