test_sparseMethods <- function(){ m <- matrix(sample.int(10, 25, T), 10, 10) colnames(m) <- paste0("cell_", 1:10) rownames(m) <- paste0("gene_", 1:10) gene.sets <- list("my_list1"= paste0("gene_", 1:2), "my_list2"= paste0("gene_", 3:4)) M <- as(m, "dgCMatrix") checkEqualsNumeric(gsva(m, gene.sets), gsva(M, gene.sets)) checkEqualsNumeric(gsva(m, gene.sets, method="plage"), gsva(M, gene.sets, method="plage")) checkEqualsNumeric(gsva(m, gene.sets, method="zscore"), gsva(M, gene.sets, method="zscore")) checkEqualsNumeric(gsva(m, gene.sets, method="ssgsea"), gsva(M, gene.sets, method="ssgsea")) }