EasyTCGA: An R package for easy batch downloading of TCGA data from FireBrowse

Abstract

Many organizations deal with the investigation of cancer including the National Institutes of Health, USA. Genomics(CCG). The Cancer Genome Atlas (TCGA) is an establishment of the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) that has created maps of the key genomic changes in more than 30 cancer types. The aim of TCGA is the improvement of the effectiveness to diagnose, to treat and to guard against cancer through genome analysis. TCGA provides a publically available dataset. The Broad Institute TCGA GDAC Firehose arranges this data set that can be loaded directly with use of FireBrowse. FireBrowse allows simple and smart download and study TCGA data and TCGA analyses. The data is downloaded as zip files. Mario Deng created an R client called FirebrowseR with the objective of getting the TCGA data from FireBrowse conveniently. The size of record sets to download is limited. EasyTCGA is an R package providing easy batch downloading of particular TCGA data from FireBrowse using FirebrowseR. The key advantage of EasyTCGA is the downloading of the whole available data set you are interested in at once as a single data frame. The focus of this technical report is on the presentation of the R package EasyTCGA . That is why all specific expressions and variables like biological data and the like will not be explained. You get all relevant background informations on the given URL’s. EasyTGCA can download clinical data, sample-level log2 miRSeq and mRNASeq expression values, selected columns from the MAF (Mutation Annotation File) generated by MutSig and significantly mutated genes, as scored by MutSig.