loadAlleleCounts: Function to load tumour allele counts from a text file or data.frame

Description

Function to load in the allele counts from tumour sequencing data from a delimited text file or data.frame object.

Usage

loadAlleleCounts(inCounts, symmetric = TRUE, genomeStyle = "NCBI", sep = "\t", header = TRUE)

Arguments

inCounts

Full file path to text file or data.frame containing tumour allele count data. inCounts must be 6 columns: chromosome, position, reference base, reference read counts, non-reference base, non-reference read counts. ‘chromosome’ column can be in ‘NCBI’ or ‘UCSC’ genome style; only autosomes, sex chromosomes, and mitochondrial chromosome are included (e.g. 1-22,X,Y,MT). The reference and non-reference base columns can be any arbitrary character; it is not used by TitanCNA.

symmetric

logical; if TRUE, then the symmetric allelic counts will be used. ref will equal max(ref,nonRef). This parameter must be the same as the symmetric parameter for loadDefaultParameters.

genomeStyle

The genome style to use for chromosomes by TitanCNA. Use one of ‘NCBI’ or ‘UCSC’. It does not matter what style is found in inCounts, genomeStyle will be the style returned.

sep

Character indicating the delimiter used for the columns for infile. Default is tab-delimited, "\t".

header

logical to indicate if the input tumour counts file contains a header line.

Value

chr: Chromosome; character, NCBI or UCSC genome style format
posn: Position; integer
ref: Reference counts; numeric
nonRef: Non-reference counts; numeric
tumDepth: Tumour depth; numeric

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)

Examples

Run this code

  infile <- system.file("extdata", "test_alleleCounts_chr2.txt", 
                        package = "TitanCNA")
  #### LOAD DATA FROM TEXT FILE ####
  data <- loadAlleleCounts(infile, symmetric = TRUE, 
  		genomeStyle = "NCBI", header = TRUE)
  
  ## Not run: 
# 	countsDF <- extractAlleleReadCounts(tumBam, tumBamIndex, 
# 			germlineHetPosns, outputFilename = NULL, 
# 			pileupParam = PileupParam())
# 	data <- loadAlleleCounts(countsDF, symmetric = TRUE, 
#   			genomeStyle = "NCBI")
#   ## End(Not run)