getGISTICPeaks: Download GISTIC2 peak-level data from the Firehose pipeline

In mksamur/RTCGAToolbox: A new tool for exporting TCGA Firehose data

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]

mksamur/RTCGAToolbox documentation built on Oct. 29, 2023, 10:06 p.m.