Description Usage Arguments Value
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | 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
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