biocExtract: Extract and convert data from a 'FirehoseData' object to a...

In RTCGAToolbox: A new tool for exporting TCGA Firehose data

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-class for more details.

Usage

biocExtract(
  object,
  type = c("clinical", "RNASeqGene", "RNASeq2Gene", "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.
...	Additional arguments passed to lower level functions that convert tabular data into Bioconductor object such as .makeRangedSummarizedExperimentFromDataFrame or .makeRaggedExperimentFromDataFrame

Details

A typical additional argument for this function passed down to lower level functions is the names.field which indicates the row names in the data. By default, it is the "Hugo_Symbol" column in the internal code that converts data.frames to SummarizedExperiment representations (via the .makeSummarizedExperimentFromDataFrame internal function).

Value

Either an SummarizedExperiment object or a RaggedExperiment object.

type

Choices include:

• clinical - Get the clinical data slot

• RNASeqGene - RNASeqGene - RNASeq v1

• RNASeqGene - RNASeq2Gene - RNASeq v2

• RNASeq2GeneNorm - RNASeq v2 Normalized

• miRNASeqGene - micro RNA SeqGene

• CNASNP - Copy Number Alteration

• CNVSNP - Copy Number Variation

• CNASeq - Copy Number Alteration

• CNACGH - Copy Number Alteration

• Methylation - Methylation

• mRNAArray - Messenger RNA

• miRNAArray - micro RNA

• RPPAArray - Reverse Phase Protein Array

• Mutation - Mutations

• GISTICA - GISTIC v2 ('AllByGene' only)

• GISTICT - GISTIC v2 ('ThresholdedByGene' only)

• GISTICP - GISTIC v2 ('Peaks' only)

• GISTIC - GISTIC v2 scores, probabilities, and peaks

Author(s)

Marcel Ramos [e-mail]

Examples

data(accmini)
biocExtract(accmini, "RNASeq2Gene")
biocExtract(accmini, "miRNASeqGene")
biocExtract(accmini, "RNASeq2GeneNorm")
biocExtract(accmini, "CNASNP")
biocExtract(accmini, "CNVSNP")
biocExtract(accmini, "Methylation")
biocExtract(accmini, "Mutation")
biocExtract(accmini, "RPPAArray")
biocExtract(accmini, "GISTIC")

RTCGAToolbox documentation built on Nov. 8, 2020, 5:34 p.m.