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,
  specificity.weight = 5,
  weight.explained = 0.5,
  max.genes = 200
)

Arguments

nmf.res

A list of NMF models obtained using multiNMF()

specificity.weight

A parameter controlling how specific gene should be for each program. 'specificity.weight=0' no constraint on specificity, and positive values impose increasing specificity.

weight.explained

Fraction of NMF weights explained by selected genes. For example if weight.explained=0.5, all genes that together account for 50% of NMF weights are used to return program signatures.

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)