getLinks {RTCGAToolbox} | R Documentation |
This function provides a reference to the resources downloaded from the GDAC Firehose pipeline. Based on the input, the function returns a URL location to the resource if there exists one.
getLinks( dataset, data_date = "20160128", RNASeqGene = FALSE, RNASeq2Gene = FALSE, clinical = FALSE, miRNASeqGene = FALSE, RNASeq2GeneNorm = FALSE, CNASNP = FALSE, CNVSNP = FALSE, CNASeq = FALSE, CNACGH = FALSE, Methylation = FALSE, Mutation = FALSE, mRNAArray = FALSE, miRNAArray = FALSE, RPPAArray = FALSE, GISTIC = FALSE )
dataset |
A cohort name. TCGA cancer code obtained via |
data_date |
Either a runDate or analysisDate typically entered in 'getFirehoseData' |
RNASeqGene |
Logical (default FALSE) RNAseq TPM data. |
RNASeq2Gene |
Logical (default FALSE) RNAseq v2 (RSEM processed) data; see |
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 |
A character URL to a dataset location