getGISTICPeaks {RTCGAToolbox} | R Documentation |
Access GISTIC2 level 4 copy number data through
gdac.broadinstitute.org
getGISTICPeaks(dataset, peak = c("wide", "narrow", "full"), rm.chrX = TRUE, gistic2Date = "20160128", destdir = tempdir())
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()) |
A data.frame
of peak values
Ludwig Geistlinger
co <- getGISTICPeaks("COAD", "wide") class(co) head(co)[1:6]