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Last data update: 2014.03.03

R: Correct for GC bias

correctCoverageBias

R Documentation

Correct for GC bias

Description

Takes as input coverage data in GATK format (or data read by readCoverageGatk) and a mapping file for GC content, and then uses a loess normalization for bias correction. Largely follows the GC correction of the TitanCNA package.

Usage

correctCoverageBias(gatk.coverage.file, gc.gene.file, 
    output.file = NULL)

Arguments

`gatk.coverage.file`	Exon coverage file as produced by GATK. Either a file name or data parsed with the readCoverageGatk function.
`gc.gene.file`	File providing GC content for each exon in the coverage files. First column in format CHR:START-END. Second column GC content (0 to 1). Third column provides gene symbols, which are optional, but used in runAbsoluteCN to generate gene level calls.
`output.file`	Optionally, write minimal GATK coverage file with GC corrected coverage.

Value

GC normalized coverage.

Author(s)

Markus Riester

Examples

gatk.normal.file <- system.file("extdata", "example_normal.txt", 
    package="PureCN")
gc.gene.file <- system.file("extdata", "example_gc.gene.file.txt", 
    package="PureCN")
coverage <- correctCoverageBias(gatk.normal.file, gc.gene.file)

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 'demo()' for some demos, 'help()' for on-line help, or
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> library(PureCN)
Loading required package: DNAcopy
Loading required package: VariantAnnotation
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: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PureCN/correctCoverageBias.Rd_%03d_medium.png", width=480, height=480)
> ### Name: correctCoverageBias
> ### Title: Correct for GC bias
> ### Aliases: correctCoverageBias
> 
> ### ** Examples
> 
> gatk.normal.file <- system.file("extdata", "example_normal.txt", 
+     package="PureCN")
> gc.gene.file <- system.file("extdata", "example_gc.gene.file.txt", 
+     package="PureCN")
> coverage <- correctCoverageBias(gatk.normal.file, gc.gene.file)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>