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]