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

Arguments

normal.coverage.files

A set of normal coverage samples to estimate target log-ratio standard deviations.

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)

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


[Package PureCN version 1.10.0 Index]