getLinks: Get resource links from inputs

In RTCGAToolbox: A new tool for exporting TCGA Firehose data

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

RTCGAToolbox documentation built on Nov. 8, 2020, 5:34 p.m.