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", "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.frame`s 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 marcel.ramos@roswellpark.org

### 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")

[Package RTCGAToolbox version 2.20.0 Index]