tests/testthat/test-runEnrichPathways.R

In ncats/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

for (rampDB in test_databases) {
  test_that("enrichment in mixed data returns correctly formatted output", {

    analytes <- c(
      "ensembl:ENSG00000135679",
      "hmdb:HMDB0000064",
      "hmdb:HMDB0000148",
      "ensembl:ENSG00000141510"
    )
    result <- runEnrichPathways(db = rampDB, analytes = analytes)
    expect_equal(
      (length(result) > 1),
      TRUE
    )
    expect_equal(
      class(result[[1]]),
      "data.frame"
    )
    expect_equal(
      (ncol(result[[1]]) > 5),
      TRUE
    )
  })


  test_that("enrichment in metabolite data returns correctly formatted output", {

    analytes <- c(
      "hmdb:HMDB0000064",
      "hmdb:HMDB0000148"
    )
    result <- runEnrichPathways(db = rampDB, analytes = analytes)
    expect_equal(
      (length(result) > 1),
      TRUE
    )
    expect_equal(
      class(result[[1]]),
      "data.frame"
    )
    expect_equal(
      (ncol(result[[1]]) > 5),
      TRUE
    )
  })


  test_that("enrichment in gene data returns correctly formatted output", {

    genes <- c(
      "ensembl:ENSG00000135679",
      "ensembl:ENSG00000141510"
    )

    result <- runEnrichPathways(db = rampDB, analytes = genes)
    expect_equal(
      (length(result) > 1),
      TRUE
    )
    expect_equal(
      class(result[[1]]),
      "data.frame"
    )
    expect_equal(
      (ncol(result[[1]]) > 5),
      TRUE
    )
  })
}