test_delayed <- function(){ set.seed(1001) m <- matrix(runif(10000), 1000, 100) rownames(m) <- paste0("gene_", 1:1000) colnames(m) <- paste0("cell_", 1:100) gene.sets <- list("my_list1"= paste0("gene_", 1:100), "my_list2"= paste0("gene_", 401:500)) h5 <- as(m, "HDF5Array") x1 <- gsva(m, gene.sets, method="plage") x2 <- gsva(h5, gene.sets, method="plage") checkEqualsNumeric(as.vector(t(x1)), as.vector(t(x2))) x1 <- gsva(m, gene.sets, method="zscore") x2 <- gsva(h5, gene.sets, method="zscore") checkEqualsNumeric(as.vector(t(x1)), as.vector(t(x2))) x1 <- gsva(m, gene.sets, method="ssgsea") x2 <- gsva(h5, gene.sets, method="ssgsea") checkEqualsNumeric(as.vector(t(x1)), as.vector(t(x2))) }