curatedTCGAData

1 Installation

source("https://bioconductor.org/biocLite.R")
BiocInstaller::biocLite("curatedTCGAData")

Load packages:

library(curatedTCGAData)
library(MultiAssayExperiment)

Checking available cancer codes and assays:

curatedTCGAData(diseaseCode = "*", assays = "*", dry.run = TRUE)

## Please see the list below for available cohorts and assays

## Available Cancer codes:
##  ACC BLCA BRCA CESC CHOL COAD DLBC ESCA GBM HNSC KICH
##  KIRC KIRP LAML LGG LIHC LUAD LUSC MESO OV PAAD PCPG
##  PRAD READ SARC SKCM STAD TGCT THCA THYM UCEC UCS UVM 
## Available Data Types:
##  CNACGH CNASNP CNASeq CNVSNP GISTICA GISTICT
##  Methylation Mutation RNASeq2GeneNorm
##  RNASeqGene RPPAArray mRNAArray miRNAArray
##  miRNASeqGene

## NULL

Check potential files to be downloaded:

curatedTCGAData(diseaseCode = "COAD", assays = "RPPA*", dry.run = TRUE)

##                COAD_RPPAArray 
## "COAD_RPPAArray-20160128.rda"