RTCGA (version 1.2.2)

getFirehoseData: Get data from Firehose portal.

Description

getFirehoseData returns FirehoseData object that stores TCGA data.

Usage

getFirehoseData(dataset, runDate = NULL, gistic2_Date = NULL,
  RNAseq_Gene = FALSE, Clinic = TRUE, miRNASeq_Gene = FALSE,
  RNAseq2_Gene_Norm = FALSE, CNA_SNP = FALSE, CNV_SNP = FALSE,
  CNA_Seq = FALSE, CNA_CGH = FALSE, Methylation = FALSE,
  Mutation = FALSE, mRNA_Array = FALSE, miRNA_Array = FALSE,
  RPPA = 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

gistic2_Date

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

RNAseq_Gene

Logical (default FALSE) parameter for RNAseq data.

Clinic

Logical (default TRUE) parameter for clinical data.

miRNASeq_Gene

Logical (default FALSE) parameter for smallRNAseq data.

RNAseq2_Gene_Norm

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

CNA_SNP

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

CNV_SNP

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

CNA_Seq

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

CNA_CGH

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.

mRNA_Array

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

miRNA_Array

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

RPPA

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)

Value

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

Details

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

Examples

#Sample Dataset
data(RTCGASample)
RTCGASample
BRCAdata <- getFirehoseData(dataset="BRCA",
runDate="20140416",gistic2_Date="20140115",
RNAseq_Gene=TRUE,Clinic=TRUE,mRNA_Array=TRUE,Mutation=TRUE)