tests/testthat/test-functions.R

In msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format

library(msigdbr)
library(dplyr)

test_that("msigdbr_species()", {
  species <- msigdbr_species()
  expect_s3_class(species, "tbl_df")
  expect_equal(nrow(species), 20)
  expect_match(species$species_name, "Homo sapiens", fixed = TRUE, all = FALSE)
  expect_match(species$species_name, "Mus musculus", fixed = TRUE, all = FALSE)
  expect_match(species$species_name, "Drosophila melanogaster", fixed = TRUE, all = FALSE)
})

test_that("msigdbr_show_species()", {
  expect_warning(msigdbr_show_species())
})

test_that("msigdbr_collections()", {
  collections <- msigdbr_collections()
  expect_s3_class(collections, "tbl_df")
  expect_gt(nrow(collections), 20)
  expect_lt(nrow(collections), 25)
  expect_match(collections$gs_cat, "C2", fixed = TRUE, all = FALSE)
  expect_match(collections$gs_cat, "C7", fixed = TRUE, all = FALSE)
  expect_match(collections$gs_subcat, "CGP", fixed = TRUE, all = FALSE)
  expect_match(collections$gs_subcat, "CP:REACTOME", fixed = TRUE, all = FALSE)
})

test_that("human gene sets overall stats", {
  msigdbr_hs <- msigdbr()
  expect_s3_class(msigdbr_hs, "tbl_df")
  expect_identical(msigdbr_hs, msigdbr(species = "human"))
  expect_gt(nrow(msigdbr_hs), 4200000)
  expect_identical(colnames(msigdbr_hs)[1:6], c("gs_cat", "gs_subcat", "gs_name", "gene_symbol", "entrez_gene", "ensembl_gene"))
  expect_gt(n_distinct(msigdbr_hs$gene_symbol), 40000)
  expect_gt(n_distinct(msigdbr_hs$entrez_gene), 40000)
  expect_gt(n_distinct(msigdbr_hs$ensembl_gene), 40000)
  expect_equal(min(rle(msigdbr_hs$gs_id)$lengths), 5)
  expect_lt(max(rle(msigdbr_hs$gs_id)$lengths), 2800)
  expect_lt(quantile(rle(msigdbr_hs$gs_id)$lengths, 0.999), 2000)
  msigdbr_hs_sym <- distinct(msigdbr_hs, gs_id, gene_symbol)
  expect_gt(nrow(msigdbr_hs_sym), 3800000)
  expect_lt(max(rle(msigdbr_hs_sym$gs_id)$lengths), 2005)
})

test_that("mouse gene sets overall stats", {
  msigdbr_mm <- msigdbr(species = "Mus musculus")
  expect_s3_class(msigdbr_mm, "tbl_df")
  expect_identical(msigdbr_mm, msigdbr(species = "mouse"))
  expect_gt(nrow(msigdbr_mm), 3700000)
  expect_identical(colnames(msigdbr_mm)[1:6], c("gs_cat", "gs_subcat", "gs_name", "gene_symbol", "entrez_gene", "ensembl_gene"))
  expect_gt(n_distinct(msigdbr_mm$human_gene_symbol), 18000)
  expect_gt(n_distinct(msigdbr_mm$gene_symbol), 17000)
  expect_gt(n_distinct(msigdbr_mm$entrez_gene), 17000)
  expect_gt(n_distinct(msigdbr_mm$ensembl_gene), 17000)
  expect_equal(max(msigdbr_mm$num_ortholog_sources), 12)
})

test_that("rat gene sets overall stats", {
  msigdbr_rn <- msigdbr(species = "Rattus norvegicus")
  expect_s3_class(msigdbr_rn, "tbl_df")
  expect_identical(msigdbr_rn, msigdbr(species = "rat"))
  expect_gt(nrow(msigdbr_rn), 3600000)
  expect_gt(n_distinct(msigdbr_rn$human_gene_symbol), 15000)
  expect_gt(n_distinct(msigdbr_rn$gene_symbol), 15000)
  expect_equal(max(msigdbr_rn$num_ortholog_sources), 10)
})

test_that("human hallmark category", {
  msigdbr_hs_h <- msigdbr(species = "Homo sapiens", category = "H")
  expect_s3_class(msigdbr_hs_h, "tbl_df")
  expect_gt(nrow(msigdbr_hs_h), 5000)
  expect_equal(length(unique(msigdbr_hs_h$gs_cat)), 1)
  expect_equal(length(unique(msigdbr_hs_h$gs_subcat)), 1)
  expect_equal(length(unique(msigdbr_hs_h$gs_id)), 50)
})

test_that("mouse hallmark category", {
  msigdbr_mm_h <- msigdbr(species = "Mus musculus", category = "H")
  expect_s3_class(msigdbr_mm_h, "tbl_df")
  expect_gt(nrow(msigdbr_mm_h), 5000)
  expect_equal(length(unique(msigdbr_mm_h$gs_cat)), 1)
  expect_equal(length(unique(msigdbr_mm_h$gs_subcat)), 1)
  expect_equal(length(unique(msigdbr_mm_h$gs_id)), 50)
})

test_that("human CGP subcategory", {
  msigdbr_hs_cgp <- msigdbr(species = "Homo sapiens", category = "C2", subcategory = "CGP")
  expect_s3_class(msigdbr_hs_cgp, "tbl_df")
  expect_gt(nrow(msigdbr_hs_cgp), 100000)
  expect_equal(length(unique(msigdbr_hs_cgp$gs_cat)), 1)
  expect_equal(length(unique(msigdbr_hs_cgp$gs_subcat)), 1)
  expect_gt(length(unique(msigdbr_hs_cgp$gs_id)), 3000)
  expect_lt(length(unique(msigdbr_hs_cgp$gs_id)), 5000)
})

test_that("human BP subcategory", {
  msigdbr_hs_bp <- msigdbr(species = "Homo sapiens", category = "C5", subcategory = "BP")
  expect_s3_class(msigdbr_hs_bp, "tbl_df")
  expect_gt(nrow(msigdbr_hs_bp), 100000)
  expect_equal(length(unique(msigdbr_hs_bp$gs_cat)), 1)
  expect_equal(length(unique(msigdbr_hs_bp$gs_subcat)), 1)
  expect_gt(length(unique(msigdbr_hs_bp$gs_id)), 7000)
  expect_lt(length(unique(msigdbr_hs_bp$gs_id)), 9000)
})

test_that("rat BP subcategory", {
  msigdbr_rn_bp <- msigdbr(species = "Rattus norvegicus", category = "C5", subcategory = "BP")
  expect_s3_class(msigdbr_rn_bp, "tbl_df")
  expect_gt(nrow(msigdbr_rn_bp), 100000)
  expect_equal(length(unique(msigdbr_rn_bp$gs_cat)), 1)
  expect_equal(length(unique(msigdbr_rn_bp$gs_subcat)), 1)
  expect_gt(length(unique(msigdbr_rn_bp$gs_id)), 7000)
  expect_lt(length(unique(msigdbr_rn_bp$gs_id)), 9000)
})

test_that("subcategory partial match", {
  msigdbr_mm_gomf <- msigdbr(species = "Mus musculus", category = "C5", subcategory = "GO:MF")
  expect_s3_class(msigdbr_mm_gomf, "tbl_df")
  msigdbr_mm_mf <- msigdbr(species = "Mus musculus", category = "C5", subcategory = "MF")
  expect_s3_class(msigdbr_mm_mf, "tbl_df")
  expect_equal(nrow(msigdbr_mm_gomf), nrow(msigdbr_mm_mf))
  expect_identical(msigdbr_mm_gomf, msigdbr_mm_mf)
})

test_that("specific genes present", {
  msigdbr_hs <- msigdbr()
  expect_gt(nrow(filter(msigdbr_hs, gene_symbol == "NRAS")), 100)
  expect_gt(nrow(filter(msigdbr_hs, gene_symbol == "PIK3CA")), 100)
  expect_equal(nrow(filter(msigdbr_hs, gs_id == "M30055", gene_symbol == "FOS")), 1)
  expect_equal(nrow(filter(msigdbr_hs, gs_id == "M30055", entrez_gene == 2353)), 1)
  expect_equal(nrow(filter(msigdbr_hs, gs_id == "M30055", ensembl_gene == "ENSG00000170345")), 1)
  expect_equal(nrow(filter(msigdbr_hs, gs_id == "M40827", gene_symbol == "ABCA11P")), 1)
  expect_equal(nrow(filter(msigdbr_hs, gs_id == "M40827", entrez_gene == 79963)), 1)
  expect_equal(nrow(filter(msigdbr_hs, gs_id == "M40827", ensembl_gene == "ENSG00000251595")), 1)
  expect_equal(nrow(filter(msigdbr_hs, gs_id == "M8918", gene_symbol == "NEPNP")), 1)
  expect_equal(nrow(filter(msigdbr_hs, gs_id == "M8918", entrez_gene == 442253)), 1)
  expect_equal(nrow(filter(msigdbr_hs, gs_id == "M8918", ensembl_gene == "ENSG00000218233")), 1)
})

test_that("number of genes in specific gene sets", {
  msigdbr_hs <- msigdbr()
  msigdbr_hs_sym <- distinct(msigdbr_hs, gs_id, gene_symbol)
  msigdbr_mm <- msigdbr(species = "Mus musculus")
  expect_equal(nrow(filter(msigdbr_hs_sym, gs_id == "M5902")), 161)
  expect_equal(nrow(filter(msigdbr_mm, gs_id == "M5902")), 161)
  expect_equal(nrow(filter(msigdbr_hs_sym, gs_id == "M5903")), 32)
  expect_equal(nrow(filter(msigdbr_mm, gs_id == "M5903")), 32)
  expect_equal(nrow(filter(msigdbr_hs_sym, gs_id == "M39207")), 5)
  expect_equal(nrow(filter(msigdbr_mm, gs_id == "M39207")), 5)
  expect_equal(nrow(filter(msigdbr_hs_sym, gs_id == "M40020")), 12)
  expect_equal(nrow(filter(msigdbr_mm, gs_id == "M40020")), 12)
  expect_equal(nrow(filter(msigdbr_hs, gs_id == "M490")), 57)
  expect_equal(nrow(filter(msigdbr_hs_sym, gs_id == "M490")), 55)
  expect_gt(nrow(filter(msigdbr_mm, gs_id == "M490")), 50)
  expect_lt(nrow(filter(msigdbr_mm, gs_id == "M490")), 60)
  expect_equal(nrow(filter(msigdbr_hs, gs_id == "M40180")), 91)
  expect_equal(nrow(filter(msigdbr_hs_sym, gs_id == "M40180")), 91)
  expect_gt(nrow(filter(msigdbr_mm, gs_id == "M40180")), 80)
  expect_lt(nrow(filter(msigdbr_mm, gs_id == "M40180")), 95)
})

test_that("wrong msigdbr() parameters", {
  expect_error(msigdbr(species = "test"))
  expect_error(msigdbr(species = c("Homo sapiens", "Mus musculus")))
  expect_error(msigdbr(species = "Homo sapiens", category = "X"))
  expect_error(msigdbr(species = "Homo sapiens", category = "X", subcategory = "X"))
  expect_error(msigdbr(species = "Homo sapiens", category = "H", subcategory = "H"))
  expect_error(msigdbr(species = "Homo sapiens", category = c("C1", "C2")))
  expect_error(msigdbr(species = "Homo sapiens", category = "C2", subcategory = c("CGP", "CP")))
})