makeSummarizedExperimentFromGISTIC: Create a SummarizedExperiment from FireHose GISTIC

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

Create a SummarizedExperiment from FireHose GISTIC

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 = c("AllByGene", "ThresholdedByGene", "Peaks"),
  rownameCol = "Gene.Symbol",
  ...
)

Arguments

gistic	A FirehoseGISTIC-class object
dataType	character(1) One of "ThresholdedByGene" (default), "AllByGene", or "Peaks"
rownameCol	character(1) The name of the column in the data to use as rownames in the data matrix (default: 'Gene.Symbol'). The row names are only set when the column name is found in the data and all values are unique.
...	Additional arguments passed to 'getGISTICPeaks'.

Value

A SummarizedExperiment object

Author(s)

L. Geistlinger, M. Ramos

Examples

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

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