annotateGeneSetMembership: Annotates rows of a data.frame with geneset membership from a...

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

Annotates rows of a data.frame with geneset membership from a GeneSetDb

Description

This is helpful when you don't have a monsterly sized GeneSetDb. There will be as many new columns added to x as there are active genesets in gdb.

Usage

annotateGeneSetMembership(x, gdb, x.ids = NULL, ...)

Arguments

x	A data.frame with genes/features in rows
gdb	A GeneSetDb() object with geneset membership
x.ids	The name of the column in x that holds the feautre id's in x that match the feature_id's in gdb, or a vector of id's to use for each row in x that represent these.
...	parameters passed down into incidenceMatrix()

Value

Returns the original x with additional columns: each is a logical vector that indicates membership for genesets defined in gdb.

Examples

vm <- exampleExpressionSet()
gdb <- exampleGeneSetDb()
mg <- seas(vm, gdb, design = vm$design, contrast = 'tumor')
lfc <- logFC(mg)
annotated <- annotateGeneSetMembership(lfc, gdb, 'feature_id')

## Show only genes that are part of 'HALLMARK_ANGIOGENESIS' geneset
angio <- subset(annotated, `c2;;BIOCARTA_AGPCR_PATHWAY`)

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