Calculate exon weights

Description

Creates an exon weight file useful for segmentation. Requires a set of GATK coverage files from normal samples. A small number of tumor (or other normal) samples is then tested against all normals. Exon weights will be set proportional to the inverse of coverage standard deviation across all normals. Exons with high variance in coverage in the pool of normals are thus down-weighted.

Usage

createExonWeightFile(gatk.tumor.files, gatk.normal.files, 
    exon.weight.file)

Arguments

Value

A data.frame with exon weights.

Author(s)

Markus Riester

Examples

exon.weight.file <- "exon_weights.txt"
gatk.normal.file <- system.file("extdata", "example_normal.txt", 
    package="PureCN")
gatk.normal2.file <- system.file("extdata", "example_normal2.txt", 
    package="PureCN")
gatk.normal.files <- c(gatk.normal.file, gatk.normal2.file)
gatk.tumor.file <- system.file("extdata", "example_tumor.txt", 
    package="PureCN")

createExonWeightFile(gatk.tumor.file, gatk.normal.files, exon.weight.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/createExonWeightFile.Rd_%03d_medium.png", width=480, height=480)
> ### Name: createExonWeightFile
> ### Title: Calculate exon weights
> ### Aliases: createExonWeightFile
> 
> ### ** Examples
> 
> exon.weight.file <- "exon_weights.txt"
> gatk.normal.file <- system.file("extdata", "example_normal.txt", 
+     package="PureCN")
> gatk.normal2.file <- system.file("extdata", "example_normal2.txt", 
+     package="PureCN")
> gatk.normal.files <- c(gatk.normal.file, gatk.normal2.file)
> gatk.tumor.file <- system.file("extdata", "example_tumor.txt", 
+     package="PureCN")
> 
> createExonWeightFile(gatk.tumor.file, gatk.normal.files, exon.weight.file)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>