getFirehoseData: Get data from Firehose portal.

In RTCGAToolbox: A new tool for exporting TCGA Firehose data

Description

getFirehoseData returns FirehoseData object that stores TCGA data.

Usage

getFirehoseData(
  dataset,
  runDate = "20160128",
  gistic2Date = "20160128",
  RNASeqGene = FALSE,
  RNASeq2Gene = 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_count",
  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 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.
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, 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 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.

Details

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

Value

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

See Also

getLinks

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)

RTCGAToolbox documentation built on Nov. 8, 2020, 5:34 p.m.