getFirehoseData {RTCGAToolbox} | R Documentation

## Get data from Firehose portal.

### Description

`getFirehoseData` returns `FirehoseData` object that stores TCGA data.

### Usage

    getFirehoseData(dataset, runDate = "20160128",
      gistic2Date = "20160128", RNASeqGene = FALSE, clinical = TRUE,
      miRNASeqGene = FALSE, RNASeq2GeneNorm = FALSE, CNASNP = FALSE,
      CNVSNP = FALSE, CNASeq = FALSE, CNACGH = FALSE,
      Methylation = FALSE, Mutation = FALSE, mRNAArray = FALSE,
      miRNAArray = FALSE, RPPAArray = FALSE, GISTIC = FALSE,
      RNAseqNorm = "raw_counts", RNAseq2Norm = "normalized_count",
      forceDownload = FALSE, destdir = tempdir(), fileSizeLimit = 500,
      getUUIDs = FALSE, ...)

### Arguments

`dataset` | A cohort name. TCGA cancer code obtained via `getFirehoseDatasets`
`runDate` | Standard data run dates. Date list can be accessible via `getFirehoseRunningDates`
`gistic2Date` | Analysis run date for GISTIC obtained via `getFirehoseAnalyzeDates`
`RNASeqGene` | Logical (default FALSE) RNAseq data.
`clinical` | Logical (default TRUE) clinical data.
`miRNASeqGene` | Logical (default FALSE) smallRNAseq data.
`RNASeq2GeneNorm` | Logical (default FALSE) RNAseq v2 (RSEM processed) data.
`CNASNP` | Logical (default FALSE) somatic copy number alterations data from SNP array.
`CNVSNP` | Logical (default FALSE) germline copy number variants data from SNP array.
`CNASeq` | Logical (default FALSE) somatic copy number alterations data from sequencing.
`CNACGH` | Logical (default FALSE) somatic copy number alterations data from CGH.
`Methylation` | Logical (default FALSE) methylation data.
`Mutation` | Logical (default FALSE) mutation data from sequencing.
`mRNAArray` | Logical (default FALSE) mRNA expression data from microarray.
`miRNAArray` | Logical (default FALSE) miRNA expression data from microarray.
`RPPAArray` | Logical (default FALSE) RPPA data
`GISTIC` | logical (default FALSE) processed copy number data
`RNAseqNorm` | RNAseq data normalization method. (Default raw_counts)
`RNAseq2Norm` | RNAseq v2 data normalization method. (Default normalized_count)
`forceDownload` | A logic (Default FALSE) key to force download RTCGAToolbox every time. By default if you download files into your working directory once than RTCGAToolbox using local files next time.
`destdir` | Directory in which to store the resulting downloaded file. Defaults to a temporary directory given by 'tempdir()'.
`fileSizeLimit` | Files that are larger than set value (megabyte) won't be downloaded (Default: 500)
`getUUIDs` | Logical key to get UUIDs from barcode (Default: FALSE)
`...` | Additional arguments to pass down. See details.

### Details

This is a main client function to download data from Firehose TCGA portal.

The `...` argument allows for selection of GISTIC peaks when calling `getGISTICPeaks`.

### Value

A `FirehoseData` data object that stores data for selected data types.

### Examples

    # Sample Dataset
    data(RTCGASample)
    RTCGASample
    ## Not run:
    BRCAdata <- getFirehoseData(dataset="BRCA",
    runDate="20140416",gistic2Date="20140115",
    RNASeqGene=TRUE,clinical=TRUE,mRNAArray=TRUE,Mutation=TRUE)

    ## End(Not run)

[Package RTCGAToolbox version 2.16.3 Index]