TCGA2STAT (version 1.0)

TCGA2STAT-package: A TCGA Data Widget for Statistical Analysis in R

Description

A R package to acquire and preprocess TCGA (genomics and clinical) data for statistical analyses.

Details

rl{ Package: TCGA2STAT Type: Package Version: 1.0 Date: 2015-06-12 License: GPL-2 } This package contains a set of tools to obtain TCGA data as an object that can be seamlessly integrated into statistical analysis pipelines in the R environment. The data obtained is being hosted and maintained by the Broad GDAC Firehose (http://gdac.broadinstitute.org/).

Both genomics and clinical data of cancer patients can be conveniently imported and merged via one simple interface of the main function in the package: getTCGA. Users just have to specify the type of cancer, data profiling platform, and/or clinical covariates, and the specified data will be imported and processed into a gene-by-sample matrix or a list of matrices for downstream statistical analyses in R. The types of diseases and molecular platforms supported by TCGA2STAT are summarized in Appendix A of the package vignette.

See Also

getTCGA

Examples

library(TCGA2STAT)
	
	#-- Default: get the expression, all clinical data, and expression merged with 
	#   overall-survival for tumor samples
	data <- getTCGA(disease="ACC", data.type="RNASeq2")
	
	#-- Get only the expression matrix
	data <- getTCGA(disease="ACC", data.type="RNASeq", type="RPKM", clinical=FALSE)

	#-- Get expression and merged with specific clinical covariate 
	data <- getTCGA(disease="OV", data.type="RNASeq", type="RPKM", cvars="ethnicity")