tests/testthat/test-geneset-score.R

In igordot/scooter: Streamlined scRNA-Seq Analysis Pipeline

test_that("geneset score can be calculated", {
  counts <- load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata", "",
      package = "scooter"
    )
  )
  s_obj <- create_seurat_obj(
    counts_matrix = counts$`Gene Expression`,
    assay = "RNA", log_file = NULL
  )
  s_obj <- add_seurat_assay(
    seurat_obj = s_obj,
    assay = "ADT",
    counts_matrix = counts$`Antibody Capture`,
    log_file = NULL
  )
  s_obj_filt <- filter_data(
    data = s_obj,
    log_file = NULL,
    min_genes = NULL,
    max_genes = NULL,
    max_mt = 10
  )

  module_tbl <- data.frame(
    gene = c(
      "CST3", "TYROBP", "LST1",
      "AIF1", "FTL", "MALAT1",
      "LTB", "IL32", "IL7R",
      "CD2", "NAPSA", "GMFG"
    ),
    celltype = c(
      rep("cell.A", 6),
      rep("cell.B", 6)
    ),
    stringsAsFactors = FALSE
  )

  geneset <- geneset_score(
    counts_raw = as.matrix(s_obj_filt@assays$RNA@counts),
    module_tbl = module_tbl
  )

  geneset <- max_scores(scores = geneset, method = "test", threshold = 0)
  expect_equal(length(unique(geneset$module)), 2)
})