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-class` 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:

- clinical - Get the clinical data slot

- RNASeqGene - RNASeqGene

- RNASeq2GeneNorm - 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 marcel.ramos@roswellpark.org

### Examples

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

    ## End(Not run)

[Package RTCGAToolbox version 2.18.0 Index]