makeSummarizedExperimentFromGISTIC: Create a SummarizedExperiment from FireHose GISTIC

Description Usage Arguments Value Author(s) Examples

View source: R/makeSummarizedExperimentFromGISTIC.R

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

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Arguments

gistic

A FirehoseGISTIC-class object

dataType

Either one of "ThresholdedByGene", "AllByGene", "Peaks"

Value

A SummarizedExperiment object

Author(s)

L. Geistlinger, M. Ramos

Examples

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

waldronlab/BiocInterfaces documentation built on Nov. 16, 2018, 1:19 a.m.