makeSummarizedExperimentFromGISTIC: Create a SummarizedExperiment from FireHose GISTIC

In TCGAutils: TCGA utility functions for data management

Description

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.

Usage

makeSummarizedExperimentFromGISTIC(gistic, dataType, ...)

Arguments

gistic	A FirehoseGISTIC-class object
dataType	Either one of "ThresholdedByGene", "AllByGene", "Peaks"
...	Additional arguments passed to 'RTCGAToolbox::getGISTICPeaks'.

Value

A SummarizedExperiment object

Author(s)

L. Geistlinger, M. Ramos

Examples

library(RTCGAToolbox)
co <- getFirehoseData("COAD", clinical = FALSE, GISTIC = TRUE,
    destdir = tempdir())
makeSummarizedExperimentFromGISTIC(co, "AllByGene")

TCGAutils documentation built on April 17, 2021, 6:04 p.m.