extractAlleleReadCounts {TitanCNA} | R Documentation |
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).
extractAlleleReadCounts(bamFile, bamIndex, positions, outputFilename = NULL, pileupParam = PileupParam())
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 |
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 |
|
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).
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 |
Gavin Ha <gavinha@gmail.com>
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)
PileupParam
; http://samtools.sourceforge.net/
## Not run: countsDF <- extractAlleleReadCounts(bamFile, bamIndex, positions, outputFilename = NULL, pileupParam = PileupParam()) data <- loadAlleleCounts(countsDF, symmetric = TRUE, genomeStyle = "NCBI") ## End(Not run)