getLinks: Get resource links from inputs

Description Usage Arguments Value

View source: R/getLinks.R

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

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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.