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

Description Usage Arguments Value Examples

View source: R/GeneSetDb-methods.R

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

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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

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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.