subsetByFeatures: Subset a GeneSetDb to only include geneSets with specified...

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

Subset a GeneSetDb to only include geneSets with specified features.

Description

Subset a GeneSetDb to only include geneSets with specified features.

Usage

subsetByFeatures(x, features, value = c("feature_id", "x.id", "x.idx"), ...)

## S4 method for signature 'GeneSetDb'
subsetByFeatures(x, features, value = c("feature_id", "x.id", "x.idx"), ...)

Arguments

x	GeneSetDb
features	Character vector of featureIds
value	are you feature id's entered as themselves (feature_id), which is the default, or are you querying by their index into a target expression object? This is only relevant if you are working with a conform-ed GeneSetDb, and further you as a user won't likely invoke this argument, but is used internally.
...	pass through arguments

Value

A subset of x which contains only the geneSets that contain features found in featureIds

Methods (by class)

• subsetByFeatures(GeneSetDb): subset GeneSetDb by feature id's

Examples

gdb <- exampleGeneSetDb()
features <- c("55839", "8522", "29087")
(gdb.sub <- subsetByFeatures(gdb, features))

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