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(normalDB, interval.weight.file = NULL,
  top.quantile = 0.7, plot = FALSE, normal.coverage.files = NULL)

Arguments

normalDB

Database of normal samples, created with createNormalDatabase.

interval.weight.file

Output filename.

top.quantile

Cap weight at the specified quantile. Intervals with standard deviation smaller than this value won't have a higher weight than intervals at this quantile.

plot

Diagnostics plot, useful to tune parameters.

normal.coverage.files

Deprecated.

Details

This function is now automatically called by createNormalDatabase and is thus deprecated.

Value

A normalDB object with following slots added

sd$log.ratios

GRanges with all log.ratios.

sd$weights

GRanges with interval weights.

Author(s)

Markus Riester


[Package PureCN version 1.16.0 Index]