tests/testthat/test_pathway_features.R

In yigbt/multiGSEA: Combining GSEA-based pathway enrichment with multi omics data integration

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))
})