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 2.14.0 Index]