test_delayed <- function() {
DEACTIVATED("HDF5Array is not yet supported by the new API.")
message("Running unit tests for DelayedMatrix.")
## 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", verbose=FALSE)
x2 <- gsva(h5, gene.sets, method="plage", verbose=FALSE)
## SVD sign is arbitrary and implementation-dependent
checkEqualsNumeric(abs(as.vector(t(x1))), abs(as.vector(t(x2))))
x1 <- gsva(m, gene.sets, method="zscore", verbose=FALSE)
x2 <- gsva(h5, gene.sets, method="zscore", verbose=FALSE)
checkEqualsNumeric(as.vector(t(x1)), as.vector(t(x2)))
x1 <- gsva(m, gene.sets, method="ssgsea", verbose=FALSE)
x2 <- gsva(h5, gene.sets, method="ssgsea", verbose=FALSE)
checkEqualsNumeric(as.vector(t(x1)), as.vector(t(x2)))
}
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