calculateIntervalWeights {PureCN} | R Documentation

## Calculate interval weights

### Description

Creates an interval weight file useful for segmentation. Requires a set of coverage files from normal samples. Interval weights will be set proportional to the inverse of coverage standard deviation across all normals. Intervals with high variance in coverage in the pool of normals are thus down-weighted.

### Usage

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

### Arguments

`normal.coverage.files` | A set of normal coverage samples to estimate target log-ratio standard deviations.
`interval.weight.file` | Output filename.
`plot` | Diagnostics plot, useful to tune parameters.

### Value

A `data.frame` with interval weights.

### Author(s)

Markus Riester

### Examples

    interval.weight.file <- "interval_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)

    calculateIntervalWeights(normal.coverage.files, interval.weight.file)

[Package PureCN version 1.12.2 Index]