TCGA2STAT-package: TCGA2STAT: TCGA to Statistical Analysis

Description Details Author(s) See Also Examples

Description

This widget automatically downloads and processes TCGA genomics and clinical data into a format convenient for statistical analyses in the R environment.

Details

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 imported by this package is the version-stamped standardized data sets 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.

Author(s)

Ying-Wooi Wan, Genevera I. Allen, Matthew L. Anderson, Zhandong Liu

Maintainer: Ying-Wooi Wan<[email protected]>

See Also

getTCGA

Examples

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	library(TCGA2STAT)
	
	#-- Default: Get only the omics-profiles, for example RNA-SeqV2
	ACC.ov <- getTCGA(disease="ACC", data.type="RNASeq2")
	str(ACC.ov)

	#-- Get the RNA-SeqV2, all clinical data, and expression merged with 
	#   overall-survival for tumor samples
	ACC.ov.os <- getTCGA(disease = "ACC", data.type = "RNASeq2", clinical=TRUE)

	#-- Get expression and merged with specific clinical covariate 
	ACC.ov.eth <- getTCGA(disease = "ACC", data.type = "RNASeq2", clinical=TRUE, 
	                        cvars="ethnicity")
	head(ACC.ov.eth$merged.dat[,1:5])

Example output

Error: Problem connect to Firehose. Please ensure Internet connection is working.

 NULL
Error: Problem connect to Firehose. Please ensure Internet connection is working.

Error: Problem connect to Firehose. Please ensure Internet connection is working.

NULL

TCGA2STAT documentation built on May 29, 2017, 8:30 p.m.