loadTCGAdata {psichomics} | R Documentation |
TCGA data obtained via FireBrowse
loadTCGAdata( folder = getDownloadsFolder(), data = c("clinical", "junction_quantification", "RSEM_genes"), exclude = c(".aux.", ".mage-tab.", "MANIFEST.txt"), ..., download = TRUE )
folder |
Character: directory to store the downloaded archives (by
default, saves to |
data |
Character: data to load (see |
exclude |
Character: files and folders to exclude from downloading and
from loading into R (by default, exclude files containing |
... |
Arguments passed on to
|
download |
Boolean: download missing files |
A list with the loaded data, unless required files are unavailable
and download = FALSE
(if so, it returns the URL of files to download)
Other functions associated with TCGA data retrieval:
getDownloadsFolder()
,
getTCGAdataTypes()
,
isFirebrowseUp()
,
parseTCGAsampleTypes()
Other functions to load data:
loadGtexData()
,
loadLocalFiles()
,
loadSRAproject()
getTCGAcohorts() getTCGAdataTypes() ## Not run: loadTCGAdata(cohort = "ACC", data_type = "Clinical") ## End(Not run)