getPositionOverlap: Function to assign values to given chromosome-position that overlaps a list of chromosomal segments

Description

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.

Usage

getPositionOverlap(chr, posn, dataVal)

Arguments

chr

Numeric array denoting the chromosome for a list of positions. Must have the same number of elements as posn.

posn

Numeric array denoting the position in the chromosome for a list of positions. Must have the same number of elements as chr.

dataVal

data.frame containing a list of segments described with 4 columns: chromosome, start coordinate, end coordinate, value of interest (e.g. log ratio). Chromosome can be all numeric or chrX and chrY can use ‘X’ and ‘Y’.

Value

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.

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")
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)