getPositionOverlap {TitanCNA} | R Documentation |
Given a list of chromosomes and positions, uses a C-based function that searches a list of segments to find the overlapping segment. Then, takes the value (4th column in segment data.frame) of the overlapping segment and assigns to the given chromosome and position.
getPositionOverlap(chr, posn, dataVal)
chr |
|
posn |
|
dataVal |
|
Numeric array
of values from the 4th column of data.frame cnData
. Each element corresponds to a genomic location from chr
and posn
that overlapped the segment in cnData
.
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)
loadAlleleCounts
, correctReadDepth
infile <- system.file("extdata", "test_alleleCounts_chr2.txt", package = "TitanCNA") tumWig <- system.file("extdata", "test_tum_chr2.wig", package = "TitanCNA") normWig <- system.file("extdata", "test_norm_chr2.wig", package = "TitanCNA") gc <- system.file("extdata", "gc_chr2.wig", package = "TitanCNA") map <- system.file("extdata", "map_chr2.wig", package = "TitanCNA") #### LOAD DATA #### data <- loadAlleleCounts(infile) #### GC AND MAPPABILITY CORRECTION #### cnData <- correctReadDepth(tumWig, normWig, gc, map) #### READ COPY NUMBER FROM HMMCOPY FILE #### logR <- getPositionOverlap(data$chr, data$posn, cnData)