getNMFgenes {GeneNMF}

Get list of genes for each NMF program

Description

Run it over a list of NMF models obtained using multiNMF()

Usage

getNMFgenes(nmf.res, method = 0.5, max.genes = 200)

Arguments

nmf.res

A list of NMF models obtained using multiNMF()

method

Parameter passed to extractFeatures to obtain top genes for each program. When 'method' is a number between 0 and 1, it indicates the minimum relative basis contribution above which the feature is selected, i.e. how specific is a gene for a given program.

max.genes

Max number of genes for each program

Value

Returns a list of top genes for each gene program found by multiNMF()

Examples

library(Seurat)
data(sampleObj)
geneNMF_programs <- multiNMF(list(sampleObj), k=5)
geneNMF_genes <- getNMFgenes(geneNMF_programs)