createTCGA | R Documentation |
This uber functionality allows to create packages with datasets from the TCGA project.
Example of such a package created with createTCGA
is https://github.com/RTCGA/RTCGA.clinical.20160128.
Resulted package is a package of type ExperimentHubData,
it consists of regular structure like R
and man
directories and also cosists of a vignette and README.md
file where the whole
construction process is decribed. The only part which must be pre-specified by a user is a DESCRIPTION
file with additional extra records:
TCGAdataSet
, TCGAreleaseDate
(releaseDate
and dataSet
to be used in downloadTCGA
) and TCGAdataType
(a type of data to be used in readTCGA).
createTCGA( description = file.path(getwd(), "DESCRIPTION"), cohorts = sub("-counts", "", rownames(infoTCGA())), tempDir = "data_tmp", clean = FALSE )
description |
A regular DESCRIPTION file with additional extra records: |
cohorts |
Names of cancer type cohorts to be included in the package. For possible names check infoTCGA. |
tempDir |
The name of temporary directory in which the data will be stored during package creation. |
clean |
A logical: should the |
A fully equpied package, ready to be shipped on Bioconductor's ExperimentHub.
If you have any problems, issues or think that something is missing or is not clear please post an issue on https://github.com/RTCGA/RTCGA/issues.
Marcin Kosinski, m.p.kosinski@gmail.com
RTCGA website http://rtcga.github.io/RTCGA/.
Other RTCGA:
RTCGA-package
,
boxplotTCGA()
,
checkTCGA()
,
convertTCGA()
,
datasetsTCGA
,
downloadTCGA()
,
expressionsTCGA()
,
heatmapTCGA()
,
infoTCGA()
,
installTCGA()
,
kmTCGA()
,
mutationsTCGA()
,
pcaTCGA()
,
readTCGA()
,
survivalTCGA()
,
theme_RTCGA()
## Not run: # https://github.com/RTCGA/RTCGA.clinical.20160128 # RTCGA.clinical.20160128 was created with cat( readLines( 'https://raw.githubusercontent.com/RTCGA/RTCGA.clinical.20160128/master/DESCRIPTION' ), file = 'DESC', sep = '\n') createTCGA('DESC', clean = TRUE) ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.