tests/testthat/test-BASiCSEstimate.R

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

context("BASiCSEstimate")

library(scuttle)
set.seed(1)
counts <- counts(mockSCE(ncells = 30, ngenes = 100))

test_that("BASiCSEstimate works", {
    skip_if_not_installed("BASiCS")
    set.seed(1)
    spike.info <- data.frame(
        Name = rownames(counts)[1:10],
        Input = rnorm(10, 500, 200),
        stringsAsFactors = FALSE
    )
    counts <- counts[rowSums(counts) != 0, ]
    params <- expect_warning(
        BASiCSEstimate(counts, spike.info,
            verbose = FALSE,
            progress = FALSE
        ),
        "is deprecated"
    )
    expect_true(validObject(params))
})

test_that("BASiCSEstimate works without spikes", {
    skip_if_not_installed("BASiCS")
    set.seed(1)
    counts <- counts[rowSums(counts) != 0, ]
    batch <- sample(1:2, ncol(counts), replace = TRUE)
    params <- expect_warning(
        BASiCSEstimate(counts,
            batch = batch,
            verbose = FALSE, progress = FALSE
        ),
        "is deprecated"
    )
    expect_true(validObject(params))
})