doQDNAseq: Quantitative inference of copy number aberrations with DNA...

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Quantitative inference of copy number aberrations with DNA isolated from fresh or formalin-fixed tissues by shallow whole-genome sequencing (QDNAseq) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of samples can be analyzed on also very limited computer systems.

Usage

  ## S3 method for class 'FastqDataSet'
doQDNAseq(dataSet, binWidth, reference, ..., verbose=FALSE)
  ## S3 method for class 'BamDataSet'
doQDNAseq(dataSet, ..., force=FALSE, verbose=FALSE)
  ## S3 method for class 'BamDataFile'
doQDNAseq(df, binWidth, residual=TRUE, blacklist=TRUE, mappability=NA, bases=NA,
  filterAllosomes=TRUE, ..., path=".", force=FALSE, verbose=FALSE)

Arguments

dataSet, df	A FastqDataSet or a BamDataSet (or a BamDataFile.
binWidth	A positive numeric specifying the bin width (in units of kbp). Alternatively, a AnnotatedDataFrame specifying the bins.
reference	A FastaReferenceFile or a BwaIndexSet specifying the genome reference to align the FASTQ reads to.
...	Additional arguments passed to applyFilters, correctBins and normalizeBins.
force	If TRUE, cached results are ignored.
verbose	See Verbose.

Value

Returns a RdsFileSet containing QDNAseqReadCounts objects.

Author(s)

Henrik Bengtsson

References

[1] TBA.

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.