loadTCGAdata: Download and process TCGA data

In psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Description

TCGA data obtained via Firebrowse

Usage

loadTCGAdata(
  folder = getDownloadsFolder(),
  data = c("clinical", "junction_quantification", "RSEM_genes"),
  exclude = c(".aux.", ".mage-tab.", "MANIFEST.txt"),
  ...,
  download = TRUE
)

Arguments

folder	Character: directory to store the downloaded archives (by default, saves to getDownloadsFolder())
data	Character: data to load (see getTCGAdataTypes())
exclude	Character: files and folders to exclude from downloading and from loading into R (by default, exclude files containing .aux., .mage-tab. and MANIFEST.TXT)
...	Arguments passed on to queryFirebrowseData date Character: dates of the data retrieval by Firebrowse (by default, it uses the most recent data available) cohort Character: abbreviation of the cohorts (by default, returns data for all cohorts) data_type Character: data types (optional) tool Character: data produced by the selected Firebrowse tools (optional) platform Character: data generation platforms (optional) center Character: data generation centres (optional) level Integer: data levels (optional) protocol Character: sample characterization protocols (optional) page Integer: page of the results to return (optional) page_size Integer: number of records per page of results (optional) sort_by String: column used to sort the data (by default, sort by cohort)
download	Boolean: download missing files

Value

A list with the loaded data, unless required files are unavailable and download = FALSE (if so, it returns the URL of files to download)

See Also

Other functions associated with TCGA data retrieval: getDownloadsFolder(), getTCGAdataTypes(), isFirebrowseUp(), parseTCGAsampleTypes()

Other functions to load data: loadGtexData(), loadLocalFiles(), loadSRAproject()

Examples

getTCGAcohorts()
getTCGAdataTypes()
## Not run: 
loadTCGAdata(cohort = "ACC", data_type = "Clinical")

## End(Not run)

psichomics documentation built on Nov. 8, 2020, 5:44 p.m.