getFirehoseData: Firehose project data client

In RTCGAToolbox: A new tool for exporting TCGA Firehose data

Description

This function will download data from Firehose project portal for further steps. Downloaded data will be store in "FirehoseData" object and also text files will be stored in working directory.

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")

Arguments

dataset	: Dataset TCGA alias. A valid list can be accessible with "getFirehoseDatasets" funtion.
runDate	: Firehose data run date. A valid dates can be accessible with "getFirehoseRunningDates" function.
gistic2_Date	: Firehose data analyze run date. A valid dates can be accessible with "getFirehoseAnalyzeDates" function.
RNAseq_Gene	: If "TRUE" client will donwload gene lebel RNASeq data.
Clinic	: If "TRUE" client will download clinical data.
miRNASeq_Gene	: If "TRUE" client will download miRNA gene level data.
RNAseq2_Gene_Norm	: If "TRUE" client will download gene level RNASeq data from second pipeline.
CNA_SNP	: If "TRUE" client will download client will download copy number alterations data processed by SNP arrays.
CNV_SNP	: If "TRUE" client will download client will download copy number variation data processed by SNP arrays.
CNA_Seq	: If "TRUE" client will download client will download copy number alterations data processed by DNA sequencing.
CNA_CGH	: If "TRUE" client will download client will download copy number alterations data processed by CGH arrays.
Methylation	: If "TRUE" client will download methylation array data.
Mutation	: If "TRUE" client will download mutation information.
mRNA_Array	: If "TRUE" client will download gene level expression profile processed by microarrays.
miRNA_Array	: If "TRUE" client will download miRNA gene level expression profile processed by microarrays.
RPPA	: If "TRUE" client will download reverse phase protein array data.
RNAseqNorm	: RNAseq data type normalization. Default: "raw_counts". Users can set "RPKM" depends on further analysis.
RNAseq2Norm	: RNAseq2 data type normalization. Default: "normalized_count". This method uses different algorithms to determine the gene expression levels. Users can set "RPKM" depends on further analysis.

Value

This function returns a "FirehoseData" object.

Author(s)

Mehmet Kemal Samur

Examples

## Not run: a2 <- getFirehoseData(dataset="BRCA",
                  runDate="20140416",gistic2_Date="20140115",
                  RNAseq_Gene=TRUE,Clinic=TRUE,mRNA_Array=TRUE,Mutation=TRUE)
## End(Not run)

RTCGAToolbox documentation built on May 2, 2019, 5:16 p.m.