checkTCGA: Information About Datasets from TCGA Project

In RTCGA/RTCGA: The Cancer Genome Atlas Data Integration

Information About Datasets from TCGA Project

Description

The checkTCGA function let's to check

• DataSets: TCGA datasets' names for current release date and cohort.

• Dates: TCGA datasets' dates of release.

Usage

checkTCGA(what, cancerType, date = NULL)

Arguments

what	One of DataSets or Dates.
cancerType	A character of length 1 containing abbreviation (Cohort code - https://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 https://gdac.broadinstitute.org/runs/ or by using checkTCGA('Dates') function. Required format 'YYYY-MM-DD'.

Details

• If what='DataSets' enables to check TCGA datasets' names for current release date and cohort.

• If what='Dates' enables to check dates of TCGA datasets' releases.

Value

• If what='DataSets' a data.frame of available datasets' names (to pass to the downloadTCGA function) and sizes.

• If what='Dates' a vector of available dates to pass to the downloadTCGA function.

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, [e-mail]

See Also

RTCGA website https://rtcga.github.io/RTCGA/.

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)

RTCGA/RTCGA documentation built on Nov. 1, 2022, 8:15 p.m.