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

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)

Results

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> library(TitanCNA)
Loading required package: foreach
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TitanCNA/getPositionOverlap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getPositionOverlap
> ### Title: Function to assign values to given chromosome-position that
> ###   overlaps a list of chromosomal segments
> ### Aliases: getPositionOverlap
> ### Keywords: manip
> 
> ### ** 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)
titan: Loading data /home/ddbj/local/lib64/R/library/TitanCNA/extdata/test_alleleCounts_chr2.txt
> 
> #### GC AND MAPPABILITY CORRECTION ####
> cnData <- correctReadDepth(tumWig, normWig, gc, map)
Reading GC and mappability files
Slurping: /home/ddbj/local/lib64/R/library/TitanCNA/extdata/gc_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Slurping: /home/ddbj/local/lib64/R/library/TitanCNA/extdata/map_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading tumour file:/home/ddbj/local/lib64/R/library/TitanCNA/extdata/test_tum_chr2.wig
Slurping: /home/ddbj/local/lib64/R/library/TitanCNA/extdata/test_tum_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading normal file:/home/ddbj/local/lib64/R/library/TitanCNA/extdata/test_norm_chr2.wig
Slurping: /home/ddbj/local/lib64/R/library/TitanCNA/extdata/test_norm_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Correcting Tumour
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Correcting Normal
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Normalizing Tumour by Normal
> 
> #### READ COPY NUMBER FROM HMMCOPY FILE ####
> logR <- getPositionOverlap(data$chr, data$posn, cnData)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>