getFirehoseData: Get data from Firehose portal.
In mksamur/RTCGAToolbox: A new tool for exporting TCGA Firehose data

getFirehoseData

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,
  RNASeq2Gene = FALSE,
  clinical = TRUE,
  miRNASeqGene = FALSE,
  miRNASeqGeneType = c("read_count", "reads_per_million_miRNA_mapped", "cross-mapped"),
  RNASeq2GeneNorm = FALSE,
  CNASNP = FALSE,
  CNVSNP = FALSE,
  CNASeq = FALSE,
  CNACGH = FALSE,
  Methylation = FALSE,
  Mutation = FALSE,
  mRNAArray = FALSE,
  miRNAArray = FALSE,
  RPPAArray = FALSE,
  GISTIC = FALSE,
  RNAseqNorm = "raw_count",
  RNAseq2Norm = c("normalized_counts", "RSEM_normalized_log2", "raw_counts",
    "scaled_estimate"),
  forceDownload = FALSE,
  destdir = .setCache(),
  fileSizeLimit = 500,
  getUUIDs = FALSE,
  ...
)

Arguments

`dataset`	A cohort disease code. TCGA cancer codes can be 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 TPM data.
`RNASeq2Gene`	Logical (default FALSE) RNAseq v2 (RSEM processed) data; see `RNAseqNorm` argument.
`clinical`	Logical (default TRUE) clinical data.
`miRNASeqGene`	Logical (default FALSE) smallRNAseq data.
`miRNASeqGeneType`	Character (default "read_count") Indicate which type of data should be pulled from the miRNASeqGene data. Must be one of "reads_per_million_miRNA_mapped", "read_count", or "cross-mapped".
`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_count)
`RNAseq2Norm`	RNAseq v2 data normalization method. (Default normalized_count or one of RSEM_normalized_log2, raw_count, scaled_estimate)
`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 cache directory given by `RTCGAToolbox:::.setCache()`.
`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.

Details

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

To avoid unnecessary downloads, we use tools::R_user_dir("RTCGAToolbox", "cache") to set the default destdir parameter to the cached directory. To get the actual default directory, one can run RTCGAToolbox:::.setCache().

Value

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

Examples

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

## End(Not run)

mksamur/RTCGAToolbox documentation built on Oct. 29, 2023, 10:06 p.m.