Convert a list of GMT gene sets to a sparse matrix

Converts a list of named gene sets (e.g., from getGMT()) into a sparse binary matrix where rows are genes, columns are gene sets, and entries are 1 if the gene is in the set.

gmtListToSparseMat(gmtList)

Arguments

gmtList

A nested list of gene sets. Outer names are gene set names; each entry is a character vector of gene names.

Value

A sparse binary matrix with genes as rows and gene sets as columns.

Examples

# define a simple nested GMT list
gmt1 <- list(
    PathwayA = c("Gene1", "Gene2", "Gene3"),
    PathwayB = c("Gene2", "Gene4")
)
gmt2 <- list(
    PathwayC = c("Gene1", "Gene4"),
    PathwayD = c("Gene3", "Gene5")
)
# combine into a nested list
nestedList <- list(gmt1 = gmt1, gmt2 = gmt2)
# convert to sparse matrix
sparseMat <- gmtListToSparseMat(nestedList)