createTargetWeights {PureCN}R Documentation

Calculate target weights

Description

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

Usage

createTargetWeights(tumor.coverage.files, normal.coverage.files,
  target.weight.file, plot = FALSE)

Arguments

tumor.coverage.files

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

normal.coverage.files

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

target.weight.file

Output filename.

plot

Diagnostics plot, useful to tune parameters.

Value

A data.frame with target weights.

Author(s)

Markus Riester

Examples


target.weight.file <- "target_weights.txt"
normal.coverage.file <- system.file("extdata", "example_normal.txt", 
    package="PureCN")
normal2.coverage.file <- system.file("extdata", "example_normal2.txt", 
    package="PureCN")
normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)
tumor.coverage.file <- system.file("extdata", "example_tumor.txt", 
    package="PureCN")

createTargetWeights(tumor.coverage.file, normal.coverage.files, target.weight.file)


[Package PureCN version 1.8.1 Index]