PureCN (version 1.0.3)

createExonWeightFile: 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

gatk.tumor.files

A small number (1-3) of GATK tumor or normal coverage samples.

gatk.normal.files

A large number of GATK normal coverage samples (>20) to estimate exon log-ratio standard deviations. Should not overlap with files in gatk.tumor.files.

exon.weight.file

Output filename.

Value

• A data.frame with exon weights.

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)