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(dataset, peak = c("wide", "narrow", "full"),
      rm.chrX = TRUE, gistic2Date = "20160128", destdir = tempdir())

### Arguments

`dataset` | A TCGA cancer code
`peak` | The peak type, select from "wide", "narrow", "full".
`rm.chrX` | (logical default TRUE) Whether to remove observations in the X chromosome
`gistic2Date` | (character default "20160128") Data of the analysis pipeline run
`destdir` | Directory location to save the downloaded file (default tempdir())

### Value

A `data.frame` of peak values

### Author(s)

Ludwig Geistlinger

### Examples

    co <- getGISTICPeaks("COAD", "wide")
    class(co)
    head(co)[1:6]

[Package RTCGAToolbox version 2.16.3 Index]