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@igordot
igordot committed Feb 15, 2025
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314 changes: 160 additions & 154 deletions tests/testthat/test-msigdbr.R
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if (requireNamespace("msigdbdf", quietly = TRUE)) {
library(dplyr)
library(dplyr)

test_that("species variations", {
# 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("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", {
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$gs_id)), 5)
m_hs_sym <- distinct(m_hs, gs_id, gene_symbol)
expect_gt(nrow(m_hs_sym), 1000000)
})
test_that("human db human genes", {
skip_if_not_installed("msigdbdf")
m_hs <- msigdbr()
expect_s3_class(m_hs, "tbl_df")
expect_identical(m_hs, msigdbr(species = "human"))
expect_identical(m_hs, msigdbr(db_species = "hs", species = "human"))
expect_gt(nrow(m_hs), 1000000)
expect_identical(names(m_hs)[1:3], c("gene_symbol", "ncbi_gene", "ensembl_gene"))
expect_identical(names(m_hs)[4:8], c("db_gene_symbol", "db_ncbi_gene", "db_ensembl_gene", "source_gene", "gs_id"))
expect_gt(n_distinct(m_hs$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", {
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$num_ortholog_sources), 12)
})
test_that("human db mouse genes", {
skip_if_not_installed("msigdbdf")
m_mm <- msigdbr(species = "Mus musculus")
expect_s3_class(m_mm, "tbl_df")
expect_identical(m_mm, msigdbr(species = "mouse"))
expect_gt(nrow(m_mm), 1000000)
expect_gt(n_distinct(m_mm$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", {
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$num_ortholog_sources), 10)
})
test_that("human db rat genes", {
skip_if_not_installed("msigdbdf")
m_rn <- msigdbr(species = "Rattus norvegicus")
expect_s3_class(m_rn, "tbl_df")
expect_identical(m_rn, msigdbr(species = "rat"))
expect_gt(nrow(m_rn), 1000000)
expect_gt(n_distinct(m_rn$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", {
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$gs_id)), 200)
})
test_that("human hallmark category", {
skip_if_not_installed("msigdbdf")
m_hs_h <- msigdbr(species = "Homo sapiens", collection = "H")
expect_s3_class(m_hs_h, "tbl_df")
expect_gt(nrow(m_hs_h), 5000)
expect_equal(n_distinct(m_hs_h$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$gs_id)), 220)
# })
# test_that("mouse hallmark category", {
# msigdbr_mm_h <- msigdbr(species = "Mus musculus", category = "H")
# expect_s3_class(msigdbr_mm_h, "tbl_df")
# expect_gt(nrow(msigdbr_mm_h), 5000)
# expect_equal(n_distinct(msigdbr_mm_h$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 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("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("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("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")))
# deprecated parameters
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"))
})
}
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"))
})

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