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 2.24.0 Index]