Description Details Author(s) See Also Examples
This widget automatically downloads and processes TCGA genomics and clinical data into a format convenient for statistical analyses in the R environment.
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.
Ying-Wooi Wan, Genevera I. Allen, Matthew L. Anderson, Zhandong Liu
Maintainer: Ying-Wooi Wan<yingwoow@bcm.edu>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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])
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Error: Problem connect to Firehose. Please ensure Internet connection is working.
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Error: Problem connect to Firehose. Please ensure Internet connection is working.
Error: Problem connect to Firehose. Please ensure Internet connection is working.
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