tests/testthat/test-runCombinedFisherTest.R

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

test_that("enrichment in mixed data returns correctly formatted output", {
  library(properties)
  dbpass <- properties::read.properties('../../dbprops.txt')
  pkg.globals <- setConnectionToRaMP(host=dbpass$hostname, dbname=dbpass$dbname, username=dbpass$username, conpass=dbpass$conpass)
  assign("pkg.globals", pkg.globals, envir = .GlobalEnv)

  analytes <- c(
    "ensembl:ENSG00000135679",
    "hmdb:HMDB0000064",
    "hmdb:HMDB0000148",
    "ensembl:ENSG00000141510"
  )
  result <- runCombinedFisherTest(analytes = analytes, background="NULL", background_type="database")
  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", {
  library(properties)
  dbpass <- properties::read.properties('../../dbprops.txt')
  pkg.globals <- setConnectionToRaMP(host=dbpass$hostname, dbname=dbpass$dbname, username=dbpass$username, conpass=dbpass$conpass)
  assign("pkg.globals", pkg.globals, envir = .GlobalEnv)

  analytes <- c(
    "hmdb:HMDB0000064",
    "hmdb:HMDB0000148"
  )
  pathwaydfids_metabolites <- getPathwayFromAnalyte(analytes = analytes)
  result <- runCombinedFisherTest(analytes = analytes, background="NULL", background_type="database")
  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", {
  pkg.globals <- setConnectionToRaMP(
    dbname = "ramp2", username = "root", conpass = "",
    host = "localhost",
  )
  analytes <- c(
    "hmdb:HMDB0000064",
    "hmdb:HMDB0000148"
  )
  pathwaydfids_metabolites <- getPathwayFromAnalyte(analytes = analytes)
  result <- runCombinedFisherTest(analytes = analytes, background="NULL", background_type="database")
  expect_equal(
    (length(result)>1),
    TRUE
  )

  expect_equal(
    (ncol(result[[1]])>5),
    TRUE
  )
})