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

In TitanCNA: Subclonal copy number and LOH prediction from whole genome sequencing of tumours

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)

	setGenomeStyle(x, genomeStyle = "NCBI", species = "Homo_sapiens", filterExtraChr = 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.
x	character vector of chromosome names to change.
species	character denoting the species
filterExtraChr	logical; if TRUE, then will return the list of chromosomes given by extractSeqlevelsByGroup for the species and for autosomes and sex chromosomes, which means that only the major chromosomes are returned (i.e. 1:22, X, Y).

Value

loadAlleleCounts returns a data.table containing components for

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

Author(s)

Gavin Ha <[e-mail]>

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

loadDefaultParameters

Examples

  infile <- system.file("extdata", "test_alleleCounts_chr2.txt", 
                        package = "TitanCNA")
  #### LOAD DATA FROM TEXT FILE ####
  data <- loadAlleleCounts(infile, symmetric = TRUE, 
  		genomeStyle = "NCBI", header = TRUE)
  
  ## use the UCSC chromosome naming convention instead ##
  data$chr <- setGenomeStyle(data$chr, genomeStyle = "UCSC")
  ## Not run: 
	data <- loadAlleleCounts(countsDF, symmetric = TRUE, 
  			genomeStyle = "NCBI")
  
## End(Not run)

TitanCNA documentation built on Nov. 8, 2020, 8:14 p.m.