geneSets: Fetch the active (or all) gene sets from a GeneSetDb or...

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

Fetch the active (or all) gene sets from a GeneSetDb or SparrowResult

Description

Fetch the active (or all) gene sets from a GeneSetDb or SparrowResult

Usage

geneSets(x, ...)

## S4 method for signature 'GeneSetDb'
length(x)

## S4 method for signature 'GeneSetDb'
geneSets(x, active.only = is.conformed(x), ..., as.dt = FALSE)

## S4 method for signature 'GeneSetDb'
nrow(x)

## S4 method for signature 'SparrowResult'
geneSets(x, ..., as.dt = FALSE)

Arguments

x	Object to retrieve the gene set from, either a GeneSetDb or a SparrowResult.
...	pass through arguments
active.only	only look for gene sets that are "active"? Defaults to TRUE if x is conformed to a target expression object, else FALSE. conform() for further details.
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.table with geneset information.

Methods (by class)

• length(GeneSetDb): Returns the number of genesets in a GeneSetDb

• geneSets(GeneSetDb): return all genesets from a GeneSetDb

• nrow(GeneSetDb): return number of genesets in GeneSetDb

• geneSets(SparrowResult): return the active genesets from a SparrowResult

Examples

gdb <- exampleGeneSetDb()
gs <- geneSets(gdb)

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