getFirehoseData: Get data from Firehose portal.

Description Usage Arguments Details Value Examples

View source: R/getFirehoseData.R

Description

getFirehoseData returns FirehoseData object that stores TCGA data.

Usage

1
2
3
4
5
6
7
8
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,
  RNAseqNorm = "raw_counts", RNAseq2Norm = "normalized_count",
  forceDownload = FALSE, destdir = ".", fileSizeLimit = 500,
  getUUIDs = FALSE)

Arguments

dataset

A cohort name. All dataset names can be accessible via getFirehoseDatasets

runDate

Standard data run dates. Date list can be accessible via getFirehoseRunningDates

gistic2Date

Analyze running dates for GISTIC processed copy number data. Date list can be accessible via getFirehoseAnalyzeDates

RNASeqGene

Logical (default FALSE) parameter for RNAseq data.

clinical

Logical (default TRUE) parameter for clinical data.

miRNASeqGene

Logical (default FALSE) parameter for smallRNAseq data.

RNASeq2GeneNorm

Logical (default FALSE) parameter for RNAseq v2 (RSEM processed) data.

CNASNP

Logical (default FALSE) parameter for somatic copy number alterations data from SNP array.

CNVSNP

Logical (default FALSE) parameter for germline copy number variants data from SNP array.

CNASeq

Logical (default FALSE) parameter for somatic copy number alterations data from sequencing.

CNACGH

Logical (default FALSE) parameter for somatic copy number alterations data from CGH.

Methylation

Logical (default FALSE) parameter for methylation data.

Mutation

Logical (default FALSE) parameter for mutation data from sequencing.

mRNAArray

Logical (default FALSE) parameter for mRNA expression data from microarray.

miRNAArray

Logical (default FALSE) parameter for miRNA expression data from microarray.

RPPAArray

Logical (default FALSE) parameter for RPPA 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 current working directory.

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)

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.

Examples

1
2
3
4
5
6
7
8
9
# 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)

RTCGAToolbox documentation built on Nov. 17, 2017, 8:36 a.m.