ReadCountsFromBam: ReadCountsFromBam

Description Usage Arguments Value Author(s) Examples

View source: R/FolderAnalysis_functions.R

Description

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

Usage

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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

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

CNVPanelizer documentation built on Nov. 8, 2020, 6:47 p.m.