ReadCountsFromBam

bamFilenames


    Vector of sample names to be used as colums names instead of bam filepaths
  

sampleNames


    Genomic Range object as created by <code>BedToGenomicRanges</code>
  

ampliconNames


  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.
  

removeDup


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


A method that allows for the use of a collection of non-matched
normal tissue samples. Our approach uses a non-parametric bootstrap
subsampling of the available reference samples to estimate the distribution
of read counts from targeted sequencing. As inspired by random forest, this
is combined with a procedure that subsamples the amplicons associated with
each of the targeted genes. The obtained information allows us to reliably
classify the copy number aberrations on the gene level.

Thomas Wolf

CNVPanelizer

Reliable CNV detection in targeted sequencing applications

ReadCountsFromBam function

Vector of sample names to be used as colums names instead of bam filepaths

Genomic Range object as created by <code>BedToGenomicRanges</code>

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.

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

ReadCountsFromBam: ReadCountsFromBam

Description

Usage

Arguments

Value

Examples