TitanCNA (version 1.10.0)

extractAlleleReadCounts: Function to extract allele read counts from a sequence alignment (BAM) file

Description

Function to extract allele read counts from a sequence alignment (BAM) file at specific positions of interest. The positions are passed in as the file path to a file in variant call format (VCF).

Usage

extractAlleleReadCounts(bamFile, bamIndex, positions,  		outputFilename = NULL, pileupParam = PileupParam())

Arguments

bamFile

File path location to the sequencing alignment file (BAM format) from which to extract read counts.

bamIndex

File path location to the BAM index file (usually with extension .bai) corresponding to the sequencing alignment file bamFile.

positions

File path location to the variant call format (VCF) file containing the positions at which read counts are to be extracted.

outputFilename

If given, will specify the file path to which the result will be output as tab-delimited text. Otherwise, the no output is written to file.

pileupParam

PileupParam object from the Rsamtools. See Details.

Value

data.frame containing columns:

chr

Chromosome; character

position

Position; numeric

ref

Reference counts; character

refCount

Reference counts; numeric

Nref

Non-reference counts; character

NrefCount

Non-reference counts; numeric

Details

The pileupParam object allows users to specify the sequencing parameters to consider when generating the pileup from which read counts are extracted. This includes ‘max_depth’, ‘min_base_quality’, ‘min_mapq’, ‘min_nucleotide_depth’=10 (recommended), ‘min_minor_allele_depth’, ‘distinguish_strands’, ‘distinguish_nucleotides’=TRUE (must be TRUE).

References

Ha, G., Roth, A., Khattra, J., Ho, J., Yap, D., Prentice, L. M., Melnyk, N., McPherson, A., Bashashati, A., Laks, E., Biele, J., Ding, J., Le, A., Rosner, J., Shumansky, K., Marra, M. A., Huntsman, D. G., McAlpine, J. N., Aparicio, S. A. J. R., and Shah, S. P. (2014). TITAN: Inference of copy number architectures in clonal cell populations from tumour whole genome sequence data. Genome Research, 24: 1881-1893. (PMID: 25060187)

See Also

PileupParam; http://samtools.sourceforge.net/

Examples

  ## Not run: 
# 	countsDF <- extractAlleleReadCounts(bamFile, bamIndex, 
# 				positions, outputFilename = NULL, 
# 				pileupParam = PileupParam())
# 	data <- loadAlleleCounts(countsDF, symmetric = TRUE, 
#   				genomeStyle = "NCBI")
#   ## End(Not run)