--- a +++ b/tests/testthat/test_pathway_features.R @@ -0,0 +1,50 @@ +context("Pathways and feature extraction") + +test_that("transcriptomic features get mapped", { + layer <- c("transcriptome") + dbs <- c("kegg") + + df <- getMultiOmicsFeatures(dbs = dbs, layer = layer) + + expect_is(df, "list") + expect_equal(length(df), 1) + expect_identical(names(df), c("transcriptome")) + + expect_match(names(df$transcriptome), "^\\(KEGG\\)") +}) + +test_that("proteomic features get mapped", { + layer <- c("proteome") + dbs <- c("kegg") + + df <- getMultiOmicsFeatures(dbs = dbs, layer = layer) + + expect_is(df, "list") + expect_equal(length(df), 1) + expect_identical(names(df), c("proteome")) + + expect_match(names(df$proteome), "^\\(KEGG\\)") +}) + +test_that("metabolomic features get mapped", { + layer <- c("metabolome") + dbs <- c("kegg") + + df <- getMultiOmicsFeatures(dbs = dbs, layer = layer) + + expect_is(df, "list") + expect_equal(length(df), 1) + expect_identical(names(df), c("metabolome")) + + expect_match(names(df$metabolome), "^\\(KEGG\\)") +}) + + +test_that("each layer has equal length", { + dbs <- c("kegg") + df <- getMultiOmicsFeatures(dbs = dbs, organism = "hsapiens") + + expect_equal(length(df), 3) + expect_equal(length(df$transcriptome), length(df$proteome)) + expect_equal(length(df$transcriptome), length(df$metabolome)) +})