Subset and filter pathway matrix to match target genes

Filters a gene-by-pathway annotation matrix to retain only pathways with sufficient overlap with a given gene set. The result is a sparse matrix aligned to new.genes, with columns (pathways) retained only if they have at least min.genes matched genes.

getMatchedPathwayMatOld(pathMat, new.genes, min.genes = 10)

Arguments

pathMat

A sparse binary matrix of genes (rows) x pathways (columns).

new.genes

Character vector of gene names to match.

min.genes

Minimum number of overlapping genes required to keep a pathway.

Value

A sparse matrix of dimensions length(new.genes) x filtered pathways.