library(Matrix)
library(SummarizedExperiment)
library(SingleCellExperiment)
library(MultiAssayExperiment)
mae1_file <- tempfile()
se1_file <- tempfile()
sce1_file <- tempfile()
# writeH5MU
test_that("a MAE object with a single matrix can be written to H5MU", {
se <- SummarizedExperiment(matrix(rnorm(100), ncol = 5))
rownames(colData(se)) <- paste("obs-", 1:ncol(se), sep = "")
mae <- MultiAssayExperiment(list(x = se))
expect_error(writeH5MU(mae, mae1_file), NA)
})
# writeH5AD
test_that("a SE object with a single matrix can be written to H5AD", {
se <- SummarizedExperiment(matrix(rnorm(100), ncol = 5))
rownames(colData(se)) <- paste("obs-", 1:ncol(se), sep = "")
rownames(se) <- paste("var-", 1:nrow(se), sep = "")
expect_error(writeH5AD(se, se1_file), NA)
})
test_that("a SCE object with a single matrix can be written to H5AD", {
sce <- SingleCellExperiment(matrix(rnorm(100), ncol = 5))
colnames(sce) <- paste("obs-", 1:ncol(sce), sep = "")
rownames(sce) <- paste("var-", 1:nrow(sce), sep = "")
expect_error(writeH5AD(sce, sce1_file), NA)
})
test_that("a SE object with a sparse matrix can be written to H5AD", {
x <- matrix(rnorm(100), ncol = 5)
mask <- matrix(rbinom(100, 1, .5), ncol = 5)
x[as.logical(mask)] <- 0
for (mxfmt in c("dgCMatrix", "dgRMatrix")) {
x_sp <- as(x, mxfmt)
se <- SummarizedExperiment(x_sp)
rownames(colData(se)) <- paste("obs-", 1:ncol(se), sep = "")
rownames(se) <- paste("var-", 1:nrow(se), sep = "")
expect_error(writeH5AD(se, se1_file), NA)
}
})
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