loadGtexData: Download and load GTEx data

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

Description

Download and load GTEx data

Usage

loadGtexData(
  folder = getDownloadsFolder(),
  data = getGtexDataTypes(),
  tissue = NULL,
  release = getGtexReleases()[[1]],
  progress = TRUE
)

Arguments

folder	Character: folder containing data
data	Character: data types to load (see getGtexDataTypes)
tissue	Character: tissues to load (if NULL, load all); tissue selection may speed up data loading
release	Numeric: GTEx data release to load
progress	Boolean: display progress?

Value

List with loaded data

See Also

Other functions associated with GTEx data retrieval: getDownloadsFolder(), getGtexDataTypes(), getGtexTissues()

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

Examples

## Not run: 
# Download and load all available GTEx data
data <- loadGtexData()

# Download and load only junction quantification and sample info from GTEx
getGtexDataTypes()
data <- loadGtexData(data=c("sampleInfo", "junctionQuant"))

# Download and load only data for specific tissues
getGtexTissues()
data <- loadGtexData(tissue=c("Stomach", "Small Intestine"))

# Download and load data from a specific GTEx data release
data <- loadGtexData(tissue=c("Stomach", "Small Intestine"), release=7)

## End(Not run)

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