This widget automatically downloads and processes TCGA genomics and clinical data into a format convenient for statistical analyses in the R environment.
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<[email protected]>
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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])
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