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 1.14.2 Index]