callAberrations {copynumber} | R Documentation

## Call aberrations in segmented data

### Description

Segments, obtained by `pcf` or `multipcf`, are classified as "gain", "normal" or "loss" given the specified thresholds.

### Usage

    callAberrations(segments, thres.gain, thres.loss = -thres.gain)

### Arguments

`segments` | a data frame containing the segmentation results found by either `pcf` or `multipcf`.
`thres.gain` | a numeric value giving the threshold to be applied for calling gains.
`thres.loss` | a numeric value giving the threshold to be applied for calling losses. Default is to use the negative value of `thres.gain`.

### Details

Each region found in `segments` is classified as "gain", "normal" or "loss". Regions with gain or loss will be those segments where the segment value is above or below the value given in `thres.gain` or `thres.loss`, respectively.

### Value

A new segment data frame where the segment values have been replaced by the classification "gain", "normal" or "loss".

### Author(s)

Gro Nilsen

### Examples

    #load lymphoma data
    data(lymphoma)
    #Run pcf
    seg <- pcf(data=lymphoma,gamma=12)

    #Call gains as segments whose value is > 0.2, and losses as segments whose
    # value < -0.1
    ab.seg <- callAberrations(seg,thres.gain=0.2,thres.loss=-0.1)

[Package copynumber version 1.28.0 Index]