checkTCGA {RTCGA}R Documentation

Information about datasets from TCGA project

Description

The checkTCGA function let's to check

Usage

checkTCGA(what, cancerType, date = NULL)

Arguments

what

One of DataSets or Dates.

cancerType

A character of length 1 containing abbreviation (Cohort code - http://gdac.broadinstitute.org/) of types of cancers to check for.

date

A NULL or character specifying from which date informations should be checked. By default (date = NULL) the newest available date is used. All available dates can be checked on http://gdac.broadinstitute.org/runs/ or by using checkTCGA('Dates') function. Required format 'YYYY-MM-DD'.

Details

Value

Issues

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.

Author(s)

Marcin Kosinski, m.p.kosinski@gmail.com

See Also

RTCGA website http://rtcga.github.io/RTCGA/Download.html.

Other RTCGA: RTCGA-package, boxplotTCGA(), convertTCGA(), datasetsTCGA, downloadTCGA(), expressionsTCGA(), heatmapTCGA(), infoTCGA(), installTCGA(), kmTCGA(), mutationsTCGA(), pcaTCGA(), readTCGA(), survivalTCGA(), theme_RTCGA()

Examples


############################# 

# names for current release date and cohort
checkTCGA('DataSets', 'BRCA' )
## Not run: 
checkTCGA('DataSets', 'OV', tail(checkTCGA('Dates'))[3] )
#checkTCGA('DataSets', 'OV', checkTCGA('Dates')[5] ) # error

## End(Not run)
# dates of TCGA datasets' releases.
checkTCGA('Dates')

############################# 
## Not run: 
# TCGA datasets' names availability for 
# current release date and cancer type.

releaseDate <- '2015-08-21'
cancerTypes <- c('OV', 'BRCA')

cancerTypes %>% sapply(function(element){
  grep(x = checkTCGA('DataSets', element, releaseDate)[, 1], 
      pattern = 'humanmethylation450', value = TRUE) %>%
       as.vector()
       })
       

## End(Not run)

[Package RTCGA version 1.23.1 Index]