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 1.18.1 Index]