longtests/testthat/test-scIB_pancreas.R

In theislab/zellkonverter: Conversion Between scRNA-seq Objects

library(SingleCellExperiment)
library(BiocFileCache)

cache <- BiocFileCache(ask = FALSE)
file <- bfcrpath(cache, "https://ndownloader.figshare.com/files/24539828")
outfile <- tempfile(fileext = ".h5ad")

names <- list(
    assays = c("X", "counts"),
    colData = c("tech", "celltype", "size_factors")
)
missing <- list()

test_that("Reading H5AD works", {
    sce <- readH5AD(file)
    expect_s4_class(sce, "SingleCellExperiment")
})

sce <- suppressWarnings(readH5AD(file))

test_that("SCE is valid", {
    validateH5ADSCE(sce, names, missing)
})

test_that("Writing H5AD works", {
    writeH5AD(sce, outfile)
    expect_true(file.exists(outfile))
})

test_that("Round trip is as expected", {
    out <- readH5AD(outfile)
    expectSCE(out, sce)
})