ReadCountsFromBam: ReadCountsFromBam
In CNVPanelizer: Reliable CNV detection in targeted sequencing applications

Description Usage Arguments Value Author(s) Examples

View source: R/FolderAnalysis_functions.R

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

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

`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.

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

Thomas Wolf, Cristiano Oliveira

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