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 Merge_methylation__humanmethylation27 - all those information are included in the DESCRIPTION file. To see
the manual page for included datasets run ?methylation.20160128 in R console.
- BRCA.methylation.20160128
- COADREAD.methylation.20160128
- GBMLGG.methylation.20160128
- KIPAN.methylation.20160128
- KIRC.methylation.20160128
- KIRP.methylation.20160128
- LAML.methylation.20160128
- LGG.methylation.20160128
- LUAD.methylation.20160128
- LUSC.methylation.20160128
- OV.methylation1.20160128
- OV.methylation2.20160128
- STAD.methylation.20160128
- STES.methylation.20160128
- UCEC.methylation.20160128
Optionally, the data can be loaded through the ExperimentHub interface.
library(ExperimentHub)
eh <- ExperimentHub()
myfiles <- query(eh, "RTCGA.methylation.20160128" )
myfiles[[1]] ## load the first resource in the list
To install this package from GitHub use
library(RTCGA)
installTCGA("RTCGA.methylation.20160128")
Make sure you have Rtools installed on your computer, if you are trying devtools on Windows.
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.