featureIdMap: Fetch the featureIdMap for a 'GeneSetDb'

In lianos/sparrow: Take command of set enrichment analyses through a unified interface

Fetch the featureIdMap for a GeneSetDb

Description

The GeneSetDb has an internal data structure that is used to cross reference the feature_id's used in the database construction to the features in the expression object that is used to run GSEA methods against.

Usage

featureIdMap(x, ...)

## S4 method for signature 'GeneSetDb'
featureIdMap(x, as.dt = FALSE)

Arguments

x	the object to retrieve the featureIdMap from
...	pass through arguments
as.dt	If FALSE (default), the data.frame like thing that this funciton returns will be set to a data.frame. Set this to TRUE to keep this object as a data.table

Value

a data.frame of input feature_id's to conformed id's/rows/etc

Methods (by class)

• featureIdMap(GeneSetDb): extract featureIdMap from a GeneSetDb

Examples

gdb <- exampleGeneSetDb()
vm <- exampleExpressionSet()
gdb <- conform(gdb, vm)
fmap <- featureIdMap(gdb)

lianos/sparrow documentation built on Feb. 5, 2024, 2:58 p.m.