getPositionOverlap: Function to assign values to given chromosome-position that...

In ATLi2001/titancna: Subclonal copy number and LOH prediction from whole genome sequencing of tumours

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.

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

loadAlleleCounts, correctReadDepth

Examples

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)

ATLi2001/titancna documentation built on May 17, 2019, 10:16 a.m.