getLinks {RTCGAToolbox} | R Documentation

## Get resource links from inputs

### Description

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.

### Usage

    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
    )

### Arguments

`dataset` | A cohort name. TCGA cancer code obtained via `getFirehoseDatasets`
`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 `RNAseqNorm` argument.
`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

### Value

A character URL to a dataset location

[Package RTCGAToolbox version 2.20.0 Index]