test_that("gsnImportGSNORA works", { # Load data files: load_test_data() # Copy STLF.GSN and delete pathways data. STLF.GSN.ora <- STLF.GSN STLF.GSN.ora$pathways <- NULL # Does it fail when no pathways data is given? testthat::expect_error( gsnImportGSNORA( object = STLF.GSN.ora, pathways_data = NULL ) ) # See if it imports GSNORA data STLF.GSN.ora <- gsnImportGSNORA( object = STLF.GSN.ora, pathways_data = PW.ORA ) # Test STLF.GSN.ora object: testthat::expect_contains( object = names(STLF.GSN.ora), expected = "pathways" ) testthat::expect_false( object = is.null( STLF.GSN.ora$pathways ) ) testthat::expect_equal( object = STLF.GSN.ora$pathways$type, expected = "gsnora" ) testthat::expect_contains( object = STLF.GSN.ora$pathways$data, expected = PW.ORA ) testthat::expect_equal( object = STLF.GSN.ora$pathways$id_col, expected = "ID" ) testthat::expect_equal( object = STLF.GSN.ora$pathways$stat_col, expected = "adj.P.1S" ) testthat::expect_equal( object = STLF.GSN.ora$pathways$sig_order, expected = "loToHi" ) testthat::expect_equal( object = STLF.GSN.ora$pathways$n_col, expected = "N" ) STLF.GSN.ora$pathways <- NULL .pw.ora <- PW.ORA .pw.ora$log10P.1S <- log10( .pw.ora$P.1S ) # Import with invalid stat_col: testthat::expect_error( gsnImportGSNORA( object = STLF.GSN.ora, pathways_data = .pw.ora, id_col = "ID", stat_col = "invalid" ) ) # Do it correctly: STLF.GSN.ora <- gsnImportGSNORA( object = STLF.GSN.ora, pathways_data = .pw.ora, id_col = "ID", stat_col = "log10P.1S", sig_order = "hiToLo", n_col = "N" ) })