listSplicingAnnotations: List alternative splicing annotations

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

List alternative splicing annotations

Description

List alternative splicing annotations

Usage

listSplicingAnnotations(
  species = NULL,
  assembly = NULL,
  date = NULL,
  cache = getAnnotationHubOption("CACHE"),
  group = FALSE
)

Arguments

species	Character: filter results by species (regular expression)
assembly	Character: filter results by assembly (regular expression)
date	Character: filter results by date (regular expression)
cache	Character: path to AnnotationHub cache (used to load alternative splicing event annotation)
group	Boolean: group values based on data provider?

Value

Named character vector with splicing annotation names

See Also

Other functions for PSI quantification: filterPSI(), getSplicingEventTypes(), loadAnnotation(), plotRowStats(), quantifySplicing()

Examples

listSplicingAnnotations() # Return all alternative splicing annotations
listSplicingAnnotations(assembly="hg19") # Search for hg19 annotation
listSplicingAnnotations(assembly="hg38") # Search for hg38 annotation
listSplicingAnnotations(date="201(7|8)") # Search for 2017 or 2018 annotation

nuno-agostinho/psichomics documentation built on Feb. 11, 2024, 11:16 p.m.