tests/testthat/test-read_kallisto.R

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

dir <- system.file("extdata", package = "scpcaData")
kallisto_dir <- file.path(dir, "Breast_Cancer_3p_LT/kallisto_txome")

# expected matrix size
sce_size <- c(60666, 30339)

test_that("Check that kallisto import works", {
  sce <- read_kallisto(kallisto_dir,
    include_unspliced = FALSE
  )
  expect_s4_class(sce, "SingleCellExperiment")
  expect_equal(dim(sce), sce_size)
  # check that column names are barcodes
  col_barcode <- str_detect(colnames(sce), "^[ACGT]+$")
  expect_true(all(col_barcode))
  expect_equal(sce@metadata$mapping_tool, "kallisto")
  expect_equal(sce@metadata$transcript_type, c("spliced"))
  expect_false(is.null(sce@metadata$kallisto_version))
  expect_false(sce@metadata$include_unspliced)
})