getLinks: Get resource links from inputs
In mksamur/RTCGAToolbox: A new tool for exporting TCGA Firehose data

getLinks

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,
  RNAseq2Norm = c("normalized_counts", "RSEM_normalized_log2", "raw_counts",
    "scaled_estimate"),
  CNASNP = FALSE,
  CNVSNP = FALSE,
  CNASeq = FALSE,
  CNACGH = FALSE,
  Methylation = FALSE,
  Mutation = FALSE,
  mRNAArray = FALSE,
  miRNAArray = FALSE,
  RPPAArray = FALSE,
  GISTIC = FALSE
)

Arguments

`dataset`	A cohort disease code. TCGA cancer codes can be 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.
`RNAseq2Norm`	RNAseq v2 data normalization method. (Default normalized_count or one of RSEM_normalized_log2, raw_count, scaled_estimate)
`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