getPositionOverlap {TitanCNA} | R Documentation

## 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`.

### Author(s)

Gavin Ha <gavinha@gmail.com>

### 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)

[Package TitanCNA version 1.24.0 Index]