loadAlleleCounts {TitanCNA} | R Documentation |
Function to load in the allele counts from tumour sequencing data from a delimited text file or data.frame object.
loadAlleleCounts(inCounts, symmetric = TRUE, genomeStyle = "NCBI", sep = "\t", header = TRUE) setGenomeStyle(x, genomeStyle = "NCBI", species = "Homo_sapiens")
inCounts |
Full file path to text file or data.frame containing tumour allele count data. |
symmetric |
|
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 |
sep |
Character indicating the delimiter used for the columns for |
header |
|
x |
|
species |
|
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 |
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)
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)