getFirehoseData {RTCGAToolbox} | R Documentation |
getFirehoseData
returns FirehoseData
object that stores TCGA data.
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, GISTIC = FALSE, RNAseqNorm = "raw_counts", RNAseq2Norm = "normalized_count", forceDownload = FALSE, destdir = ".", fileSizeLimit = 500, getUUIDs = FALSE, ...)
dataset |
A cohort name. TCGA cancer code obtained via |
runDate |
Standard data run dates. Date list can be accessible via |
gistic2Date |
Analysis run date for GISTIC obtained via |
RNASeqGene |
Logical (default FALSE) RNAseq data. |
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_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) |
... |
Additional arguments to pass down. See details. |
This is a main client function to download data from Firehose TCGA portal.
The ...
argument allows for selection of GISTIC peaks
when calling getGISTICPeaks
.
A FirehoseData
data object that stores data for selected data types.
# 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)