incidenceMatrix: Creates a 1/0 matrix to indicate geneset membership to target...

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

Description

Generates an inidcator matrix to indicate membership of genes (columns) to gene sets (rows). If y is provided, then the incidence is mapped across the entire feature-space of y.

Usage

incidenceMatrix(x, y, ...)

Arguments

x	A GeneSetDb()
y	(optional) A target (expression) object x is (or can be) conformed to
...	parameters passed down into conform().

Value

incidence matrix with nrows = number of genesets and columns are featureIDs. If y is passed in, the columns of the returned value match the rows of y.

Examples

vm <- exampleExpressionSet()
gdb <- getMSigGeneSetDb('H', 'human', 'entrez')
im <- incidenceMatrix(gdb)
imv <- incidenceMatrix(gdb, vm)

lianos/multiGSEA documentation built on Nov. 17, 2020, 1:26 p.m.