makeSummarizedExperimentFromGISTIC {TCGAutils} | R Documentation |
Use the output of getFirehoseData
to create a
SummarizedExperiment. This can be done for three types of
data, G-scores thresholded by gene, copy number by gene, and copy number by
peak regions.
makeSummarizedExperimentFromGISTIC(gistic, dataType)
gistic |
A FirehoseGISTIC-class object |
dataType |
Either one of "ThresholdedByGene", "AllByGene", "Peaks" |
A SummarizedExperiment
object
L. Geistlinger, M. Ramos
library(RTCGAToolbox) co <- getFirehoseData("COAD", clinical = FALSE, GISTIC = TRUE, destdir = tempdir()) makeSummarizedExperimentFromGISTIC(co, "AllByGene")