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

In lianos/multiGSEA: A unified interface to a plethora of gene set enrichment analysis methods

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 <- multiGSEA(gdb, vm, vm$design, 'tumor', methods=NULL)
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/multiGSEA documentation built on Nov. 17, 2020, 1:26 p.m.