tests/testthat/test-bcbioSingleCell.R

In hbc/bcbioSinglecell: Bcbio Single-Cell RNA-Seq

uploadDir <- system.file("extdata/indrops", package = "bcbioSingleCell")

## Minimal mode, with no metadata or annotations.
## This is fast but doesn't slot a lot of useful info.
test_that("Minimal mode", {
    x <- bcbioSingleCell(uploadDir = uploadDir)
    expect_s4_class(x, "bcbioSingleCell")
})

test_that("User-defined metadata", {
    x <- bcbioSingleCell(
        uploadDir = uploadDir,
        sampleMetadataFile <- file.path(uploadDir, "metadata.csv")
    )
    expect_s4_class(x, "bcbioSingleCell")
})

## Automatic organism annotations from AnnotationHub.
test_that("AnnotationHub", {
    x <- bcbioSingleCell(
        uploadDir = uploadDir,
        organism = "Homo sapiens"
    )
    expect_s4_class(x, "bcbioSingleCell")
})