getGISTICPeaks {RTCGAToolbox} | R Documentation

## Download GISTIC2 peak-level data from the Firehose pipeline

### Description

Access GISTIC2 level 4 copy number data through `gdac.broadinstitute.org`

### Usage

    getGISTICPeaks(object, peak = c("wide", "narrow", "full"), rm.chrX = TRUE)

### Arguments

`object` | A FirehoseData GISTIC type object
`peak` | The peak type, select from "wide", "narrow", "full".
`rm.chrX` | (logical default TRUE) Whether to remove observations in the X chromosome

### Value

A `data.frame` of peak values

### Author(s)

Ludwig Geistlinger

### Examples

    co <- getFirehoseData("COAD", clinical = FALSE, GISTIC = TRUE)
    peaks <- getGISTICPeaks(co, "wide")
    class(peaks)
    head(peaks)[1:6]

[Package RTCGAToolbox version 2.20.0 Index]