incidence-methods {GSEABase} | R Documentation

## Methods for Constructing Incidence Matricies Between GeneSets

### Description

An incidence matrix summarizes shared membership of gene identifiers across (pairs of) gene sets.

### Methods

The return value is a matrix with rows representing gene sets and columns genes.

`signature(x="GeneSet", ...)` `signature(x="GeneColorSet", ...)`

  All additional arguments `...` are of the same class as `x`. The incidence matrix contains elements 0 (genes not present) or 1 (genes present).

`signature(x = "GeneSetCollection", ...)`

  Additional arguments `...` can be of class `GeneSetCollection` or `GeneSet`. The incidence matrix contains elements 0 (genes not present) or 1 (genes present).

### Examples

    fl <- system.file("extdata", "Broad.xml", package="GSEABase")
    gss <- getBroadSets(fl) # GeneSetCollection of 2 sets
    ## From one or more GeneSetCollections...
    imat <- incidence(gss)
    dim(imat)
    imat[,c(1:3,ncol(imat)-3+1:3)]

    ## .. or GeneSets
    imat1 <- incidence(gss[[1]], gss[[2]], gss[[1]])
    imat1[,1:5]

[Package GSEABase version 1.54.0 Index]