biocExtract {RTCGAToolbox}R Documentation

Extract and convert data from a FirehoseData object to a Bioconductor object

Description

This function processes data from a FirehoseData object. Raw data is converted to a conventional Bioconductor object. The function returns either a SummarizedExperiment or a RaggedExperiment class object. In cases where there are multiple platforms in a data type, an attempt to consolidate datasets will be made based on matching dimension names. For ranged data, this functionality is provided with more control as part of the RaggedExperiment features. See RaggedExperiment for more details.

Usage

biocExtract(object, type = c("clinical", "RNASeqGene", "miRNASeqGene",
  "RNASeq2GeneNorm", "CNASNP", "CNVSNP", "CNASeq", "CNACGH", "Methylation",
  "Mutation", "mRNAArray", "miRNAArray", "RPPAArray", "GISTIC", "GISTICA",
  "GISTICT", "GISTICP"))

Arguments

object

A FirehoseData object from which to extract data.

type

The type of data to extract from the "FirehoseData" object, see type section.

Value

Either an SummarizedExperiment object or a RaggedExperiment object.

type

Choices include:

Author(s)

Marcel Ramos marcel.ramos@roswellpark.org

Examples

## Not run: 
    coadmut <- getFirehoseData("COAD", Mutation = TRUE)
    biocExtract(coadmut, "Mutation")

## End(Not run)

[Package RTCGAToolbox version 2.14.0 Index]