FirehoseData-class {RTCGAToolbox} | R Documentation

## An S4 class to store main data object from clinent function.

### Description

An S4 class to store main data object from clinent function.

### Usage

    ## S4 method for signature 'FirehoseData'
    show(object)

    ## S4 method for signature 'FirehoseData'
    getData(object, type, platform)

    ## S4 method for signature 'FirehoseData'
    updateObject(object, ..., verbose = FALSE)

    ## S4 method for signature 'FirehoseData'
    selectType(object, dataType)

### Arguments

`object` | A FirehoseData object
`type` | A data type to be extracted
`platform` | An index for data types that may come from multiple platforms (such as mRNAArray), for GISTIC data, one of the options: 'AllByGene' or 'ThresholdedByGene'
`...` | additional arguments for updateObject
`verbose` | logical (default FALSE) whether to print extra messages
`dataType` | An available data type, see object show method

### Methods (by generic)

- `show`: show method

- `getData`: Get a matrix or data.frame from `FirehoseData`

- `updateObject`: Update an old RTCGAToolbox FirehoseData object to the most recent API

- `selectType`: Extract data type

### Slots

`Dataset`

  A cohort name

`runDate`

  Standard data run date from `getFirehoseRunningDates`

`gistic2Date`

  Analyze running date from `getFirehoseAnalyzeDates`

`clinical`

  clinical data frame

`RNASeqGene`

  Gene level expression data matrix from RNAseq

`RNASeq2GeneNorm`

  Gene level expression data matrix from RNAseq (RSEM)

`miRNASeqGene`

  miRNA expression data from matrix smallRNAseq

`CNASNP`

  A data frame to store somatic copy number alterations from SNP array platform

`CNVSNP`

  A data frame to store germline copy number variants from SNP array platform

`CNASeq`

  A data frame to store somatic copy number alterations from sequencing platform

`CNACGH`

  A list that stores `FirehoseCGHArray` object for somatic copy number alterations from CGH platform

`Methylation`

  A list that stores `FirehoseMethylationArray` object for methylation data

`mRNAArray`

  A list that stores `FirehosemRNAArray` object for gene expression data from microarray

`miRNAArray`

  A list that stores `FirehosemRNAArray` object for miRNA expression data from microarray

`RPPAArray`

  A list that stores `FirehosemRNAArray` object for RPPA data

`Mutation`

  A data frame for mutation infromation from sequencing data

`GISTIC`

  A `FirehoseGISTIC` object to store processed copy number data

`BarcodeUUID`

  A data frame that stores the Barcodes, UUIDs and Short sample identifiers

[Package RTCGAToolbox version 2.12.1 Index]