RTCGA.CNV.20160128

This package was created with RTCGA::createTCGA() function and is a part of RTCGA project. It consist of data from The Cancer Genome Atlas Project.

Datasets existing in this package were downloaded automatically from Firehose Broad GDAC portal. They were taken from the 2016-01-28 release date. All release dates are available here. Datasets were downloaded with the use of RTCGA::downloadTCGA() function and were transposed with RTCGA::readTCGA() function.

The package contains following datasets, which names corresponds to: the cohort type, data type and release date. Cohort types can be checked with RTCGA::infoTCGA(), release dates with RTCGA::checkTCGA('Dates') and data types with e.g. RTCGA::checkTCGA('DataSets', 'BRCA') calls. The used data type for this package was segmented_scna_minus_germline_cnv_hg19 - all those information are included in the DESCRIPTION file. To see the manual page for included datasets run ?CNV.20160128 in R console.

• ACC.CNV.20160128
• BLCA.CNV.20160128
• BRCA.CNV.20160128
• CESC.CNV.20160128
• CHOL.CNV.20160128
• COADREAD.CNV.20160128
• DLBC.CNV.20160128
• ESCA.CNV.20160128
• GBMLGG.CNV.20160128
• HNSC.CNV.20160128
• KICH.CNV.20160128
• KIPAN.CNV.20160128
• KIRC.CNV.20160128
• KIRP.CNV.20160128
• LAML.CNV.20160128
• LIHC.CNV.20160128
• LUAD.CNV.20160128
• LUSC.CNV.20160128
• MESO.CNV.20160128
• OV.CNV.20160128
• PAAD.CNV.20160128
• PCPG.CNV.20160128
• PRAD.CNV.20160128
• SARC.CNV.20160128
• SKCM.CNV.20160128
• STAD.CNV.20160128
• STES.CNV.20160128
• TGCT.CNV.20160128
• THCA.CNV.20160128
• THYM.CNV.20160128
• UCEC.CNV.20160128
• UCS.CNV.20160128
• UVM.CNV.20160128

Optionally, the data can be loaded through the ExperimentHub interface.

library(ExperimentHub)
eh <- ExperimentHub()
myfiles <- query(eh,  "RTCGA.CNV.20160128" )
myfiles[[1]]  ## load the first resource in the list

Installation

To install this package from GitHub use

library(RTCGA) 
 installTCGA("RTCGA.CNV.20160128") 

Make sure you have Rtools installed on your computer, if you are trying devtools on Windows.

Notes

Note that this package is a data package with datasets from 2016-01-28 release date. There are few data packages already on Bioconductor with datasets from "2015-11-01". To read more check ?RTCGA::datasetsTCGA.