Correct GC content and mappability biases in sequencing data read counts

Description

Correct GC content and mappability biases in tumour sequence read counts using Loess curve fitting. Wrapper for function in HMMcopy.

Usage

  correctReadDepth(tumWig, normWig, gcWig, mapWig, genomeStyle = "NCBI", targetedSequence = NULL)

Arguments

Details

Wrapper for correctReadcount in HMMcopy package. It uses a sampling of 50000 bins to find the Loess fit. Then, the log ratio for every bin is returned as the log base 2 of the ratio between the corrected tumour read count and the corrected normal read count.

Value

data.frame containing columns:

Author(s)

Gavin Ha <gavinha@gmail.com>, Daniel Lai <jujubix@cs.ubc.ca>, Yikan Wang <ykwang@bccrc.ca>

References

Ha, G., Roth, A., Lai, D., Bashashati, A., Ding, J., Goya, R., Giuliany, R., Rosner, J., Oloumi, A., Shumansky, K., Chin, S.F., Turashvili, G., Hirst, M., Caldas, C., Marra, M. A., Aparicio, S., and Shah, S. P. (2012). Integrative analysis of genome wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer. Genome Research, 22(10):1995,2007. (PMID: 22637570)

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

correctReadcount and wigToRangedData in the HMMcopy package. WIG: http://genome.ucsc.edu/goldenPath/help/wiggle.html

Examples

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")

#### GC AND MAPPABILITY CORRECTION ####
cnData <- correctReadDepth(tumWig, normWig, gc, map)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> 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/correctReadDepth.Rd_%03d_medium.png", width=480, height=480)
> ### Name: correctReadDepth
> ### Title: Correct GC content and mappability biases in sequencing data
> ###   read counts
> ### Aliases: correctReadDepth
> ### Keywords: IO manip
> 
> ### ** Examples
> 
> 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")
> 
> #### 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
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>