library(dplyr) test_that("species variations", { skip_if_not_installed("msigdbdf") # human genes m_hs_hs <- msigdbr() expect_s3_class(m_hs_hs, "tbl_df") expect_identical(m_hs_hs, msigdbr(species = "Homo sapiens")) expect_identical(m_hs_hs, msigdbr(db_species = "hs", species = "human")) # mouse genes m_hs_mm <- msigdbr(species = "Mus musculus") expect_s3_class(m_hs_mm, "tbl_df") expect_identical(m_hs_mm, msigdbr(db_species = "hs", species = "mouse")) # rat genes m_hs_rn <- msigdbr(species = "Rattus norvegicus") expect_s3_class(m_hs_rn, "tbl_df") # mouse database and genes m_mm_mm <- msigdbr(db_species = "mm", species = "Mus musculus") expect_s3_class(m_mm_mm, "tbl_df") # column names should be identical (extra output with orthologs) expect_identical(names(m_hs_hs)[1:19], names(m_hs_mm)[1:19]) expect_identical(names(m_hs_mm)[1:19], names(m_hs_rn)[1:19]) expect_identical(names(m_mm_mm)[1:19], names(m_hs_mm)[1:19]) # ortholog conversion should not reduce the database size substantially expect_gt(nrow(m_hs_mm), nrow(m_hs_hs) * 0.9) expect_gt(nrow(m_hs_rn), nrow(m_hs_hs) * 0.9) # non-supported combinations expect_error(msigdbr(db_species = "mm", species = "Homo sapiens")) expect_error(msigdbr(db_species = "mm", species = "human")) expect_error(msigdbr(db_species = "mm", species = "Rattus norvegicus")) }) test_that("human db human genes", { skip_if_not_installed("msigdbdf") m_hs <- msigdbr() expect_s3_class(m_hs, "tbl_df") expect_identical(m_hs, msigdbr(species = "human")) expect_identical(m_hs, msigdbr(db_species = "hs", species = "human")) expect_gt(nrow(m_hs), 1000000) expect_identical(names(m_hs)[1:3], c("gene_symbol", "ncbi_gene", "ensembl_gene")) expect_identical(names(m_hs)[4:8], c("db_gene_symbol", "db_ncbi_gene", "db_ensembl_gene", "source_gene", "gs_id")) expect_gt(n_distinct(m_hs$gs_id), 30000) expect_gt(n_distinct(m_hs$gene_symbol), 40000) expect_gt(n_distinct(m_hs$ncbi_gene), 40000) expect_gt(n_distinct(m_hs$ensembl_gene), 40000) expect_equal(min(table(m_hs$gs_id)), 5) m_hs_sym <- distinct(m_hs, gs_id, gene_symbol) expect_gt(nrow(m_hs_sym), 1000000) }) test_that("human db mouse genes", { skip_if_not_installed("msigdbdf") m_mm <- msigdbr(species = "Mus musculus") expect_s3_class(m_mm, "tbl_df") expect_identical(m_mm, msigdbr(species = "mouse")) expect_gt(nrow(m_mm), 1000000) expect_gt(n_distinct(m_mm$gs_id), 30000) expect_gt(n_distinct(m_mm$gene_symbol), 15000) expect_gt(n_distinct(m_mm$ncbi_gene), 15000) expect_gt(n_distinct(m_mm$ensembl_gene), 15000) expect_equal(max(m_mm$num_ortholog_sources), 12) }) test_that("human db rat genes", { skip_if_not_installed("msigdbdf") m_rn <- msigdbr(species = "Rattus norvegicus") expect_s3_class(m_rn, "tbl_df") expect_identical(m_rn, msigdbr(species = "rat")) expect_gt(nrow(m_rn), 1000000) expect_gt(n_distinct(m_rn$gs_id), 30000) expect_gt(n_distinct(m_rn$gene_symbol), 15000) expect_gt(n_distinct(m_rn$ncbi_gene), 15000) expect_gt(n_distinct(m_rn$ensembl_gene), 15000) expect_equal(max(m_rn$num_ortholog_sources), 10) }) test_that("human hallmark category", { skip_if_not_installed("msigdbdf") m_hs_h <- msigdbr(species = "Homo sapiens", collection = "H") expect_s3_class(m_hs_h, "tbl_df") expect_gt(nrow(m_hs_h), 5000) expect_equal(n_distinct(m_hs_h$gs_collection), 1) expect_equal(n_distinct(m_hs_h$gs_subcollection), 1) expect_equal(n_distinct(m_hs_h$gs_id), 50) expect_gt(min(table(m_hs_h$gs_id)), 30) expect_lt(max(table(m_hs_h$gs_id)), 350) m_hs_h_ncbi <- distinct(m_hs_h, gs_id, ncbi_gene) expect_gt(min(table(m_hs_h_ncbi$gs_id)), 30) expect_equal(max(table(m_hs_h_ncbi$gs_id)), 200) m_hs_h_sym <- distinct(m_hs_h, gs_id, gene_symbol) expect_gt(min(table(m_hs_h_sym$gs_id)), 30) expect_equal(max(table(m_hs_h_sym$gs_id)), 200) }) # 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(n_distinct(msigdbr_mm_h$gs_cat), 1) # expect_equal(n_distinct(msigdbr_mm_h$gs_subcat), 1) # expect_equal(n_distinct(msigdbr_mm_h$gs_id), 50) # expect_gt(min(table(msigdbr_mm_h$gs_id)), 30) # expect_lt(max(table(msigdbr_mm_h$gs_id)), 250) # msigdbr_mm_h_entrez <- distinct(msigdbr_mm_h, gs_id, entrez_gene) # expect_gt(min(table(msigdbr_mm_h_entrez$gs_id)), 30) # expect_lt(max(table(msigdbr_mm_h_entrez$gs_id)), 220) # msigdbr_mm_h_symbol <- distinct(msigdbr_mm_h, gs_id, gene_symbol) # expect_gt(min(table(msigdbr_mm_h_symbol$gs_id)), 30) # expect_lt(max(table(msigdbr_mm_h_symbol$gs_id)), 220) # }) # test_that("human CGP subcategory", { # msigdbr_hs_cgp <- msigdbr(species = "Homo sapiens", category = "C2", subcategory = "CGP") # expect_s3_class(msigdbr_hs_cgp, "tbl_df") # expect_gt(nrow(msigdbr_hs_cgp), 100000) # expect_equal(n_distinct(msigdbr_hs_cgp$gs_cat), 1) # expect_equal(n_distinct(msigdbr_hs_cgp$gs_subcat), 1) # expect_gt(n_distinct(msigdbr_hs_cgp$gs_id), 3000) # expect_lt(n_distinct(msigdbr_hs_cgp$gs_id), 5000) # }) # test_that("human BP subcategory", { # msigdbr_hs_bp <- msigdbr(species = "Homo sapiens", category = "C5", subcategory = "BP") # expect_s3_class(msigdbr_hs_bp, "tbl_df") # expect_gt(nrow(msigdbr_hs_bp), 100000) # expect_equal(n_distinct(msigdbr_hs_bp$gs_cat), 1) # expect_equal(n_distinct(msigdbr_hs_bp$gs_subcat), 1) # expect_gt(n_distinct(msigdbr_hs_bp$gs_id), 7000) # expect_lt(n_distinct(msigdbr_hs_bp$gs_id), 9000) # }) # test_that("rat BP subcategory", { # msigdbr_rn_bp <- msigdbr(species = "Rattus norvegicus", category = "C5", subcategory = "BP") # expect_s3_class(msigdbr_rn_bp, "tbl_df") # expect_gt(nrow(msigdbr_rn_bp), 500000) # expect_equal(n_distinct(msigdbr_rn_bp$gs_cat), 1) # expect_equal(n_distinct(msigdbr_rn_bp$gs_subcat), 1) # expect_gt(n_distinct(msigdbr_rn_bp$gs_id), 7000) # expect_lt(n_distinct(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("wrong parameters", { expect_error(msigdbr(db_species = "X")) expect_error(msigdbr(db_species = "RN")) expect_error(msigdbr(species = "test")) expect_error(msigdbr(species = c("Homo sapiens", "Mus musculus"))) expect_error(msigdbr(species = "")) expect_error(msigdbr(species = NA)) expect_error(msigdbr(species = "Homo sapiens", collection = "X")) expect_error(msigdbr(species = "Homo sapiens", collection = "X", subcollection = "X")) expect_error(msigdbr(species = "Homo sapiens", collection = "H", subcollection = "H")) expect_error(msigdbr(species = "Homo sapiens", collection = c("C1", "C2"))) expect_error(msigdbr(species = "Homo sapiens", collection = "C2", subcollection = c("CGP", "CP"))) }) test_that("deprecated parameters", { skip_if_not_installed("msigdbdf") expect_warning(msigdbr(species = "Homo sapiens", category = "H")) expect_warning(msigdbr(species = "Homo sapiens", subcategory = "CGP")) m_hs <- msigdbr(species = "Homo sapiens", category = "H") expect_contains(colnames(m_hs), c("gene_symbol", "entrez_gene", "ensembl_gene", "gs_cat", "gs_subcat")) })