aspectClasses: aspectClasses and subAspectClasses

In frankkramer-lab/RCX: R package implementing the Cytoscape Exchange (CX) format

aspectClasses and subAspectClasses

Description

To get the aspect classes it is advised to always use the getAspectClasses() function to ensure the correct functionality. aspectClasses and subAspectClasses contain the default RCX accession name and the classes of the corresponding (sub)aspect. The getAspectClasses() function standardizes access to the accession names and classes, and also allows to include installed extensions of the RCX data model. Only installed and loaded extensions are included in the result: New extensions should register on load using the setExtension function to be added to options()$RCX.options$extensions, and therefore to getAspectClasses().

Usage

aspectClasses

getAspectClasses(extensions = TRUE)

subAspectClasses

updateAspectClasses(aspectClasses = aspectClasses)

Arguments

extensions	logical; whether to include aspect classes from extensions
aspectClasses	named character; accession names and aspect classes

Format

An object of class character of length 14.

An object of class character of length 4.

Details

updateAspectClasses sets the default aspect classes in options()$RCX.options, either from aspectClasses or manually provided options.

Value

named character; accession names and aspect classes

See Also

setExtension

Examples

## default aspect classes
aspectClasses

## get set aspect classes from options()
aspectClasses = getAspectClasses()

## get aspect classes without extensions
aspectClasses = getAspectClasses(extensions=FALSE)

## set default updateClasses
updateAspectClasses(
  aspectClasses = aspectClasses
)

## default sub aspect classes
subAspectClasses

frankkramer-lab/RCX documentation built on Feb. 4, 2023, 5:12 p.m.