add tests

Author: bvenn

tests/BioFSharp.Stats.Tests/BioFSharp.Stats.Tests.fsproj

@@ -9,6 +9,7 @@
   </PropertyGroup>
 
   <ItemGroup>
+    <Compile Include="OntologyEnrichmentTests.fs" />
     <Compile Include="RNASeqTests.fs" />
     <Compile Include="Program.fs" />
   </ItemGroup>

tests/BioFSharp.Stats.Tests/OntologyEnrichmentTests.fs

@@ -0,0 +1,81 @@
+namespace BioFSharp.Stats.Tests
+
+open Xunit
+open BioFSharp
+open BioFSharp.Stats
+open OntologyEnrichment
+
+module OntologyEnrichmentTests =
+
+    let data =  [|
+        createOntologyItem "id01" "PS.lightreaction.LHCII;protein.degradation.ubiquitin" 1 "description01"
+        createOntologyItem "id02" "PS.lightreaction.LHCII" 0 "description02"
+        createOntologyItem "id03" "PS.lightreaction.LHCII" 1 "description03"
+        createOntologyItem "id04" "PS.lightreaction.LHCII" 0 "description04"
+        createOntologyItem "id05" "PS.lightreaction.LHCII" 0 "description05"
+        createOntologyItem "id06" "PS.lightreaction.LHCII" 1 "description06"
+        createOntologyItem "id07" "PS.lightreaction.LHCII" 0 "description07"
+        createOntologyItem "id08" "PS.lightreaction.LHCII" 1 "description08"
+        createOntologyItem "id09" "PS.lightreaction.LHCII" 0 "description09"
+        createOntologyItem "id10" "PS.lightreaction.LHCII" 1 "description10"
+        createOntologyItem "id11" "PS.lightreaction.LHCII" 0 "description11" //36
+        createOntologyItem "id12" "PS.lightreaction" 0 "description12"
+        createOntologyItem "id13" "PS.lightreaction" 0 "description13"
+        createOntologyItem "id14" "PS.lightreaction" 0 "description14"
+        createOntologyItem "id15" "PS.lightreaction" 1 "description15" //8
+        createOntologyItem "id16" "protein.degradation.ubiquitin" 0 "description16"
+        createOntologyItem "id17" "protein.degradation.ubiquitin" 1 "description17"
+        createOntologyItem "id18" "protein.degradation.ubiquitin" 0 "description18"
+        createOntologyItem "id19" "protein.degradation.ubiquitin" 0 "description19"
+        createOntologyItem "id20" "protein.degradation.ubiquitin" 1 "description20"
+        createOntologyItem "id21" "protein.degradation.ubiquitin" 0 "description21" //18
+        createOntologyItem "id22" "protein.degradation.ubiquitin.e1" 0 "description22"
+        createOntologyItem "id23" "protein.degradation.ubiquitin.e1" 0 "description23"
+        createOntologyItem "id24" "protein.degradation.ubiquitin.e1" 0 "description24" //12
+        createOntologyItem "id25" "protein.synthesis.initiation" 1 "description25"
+        createOntologyItem "id26" "protein.synthesis.initiation" 0 "description26"
+        createOntologyItem "id27" "protein.synthesis.initiation" 1 "description27"
+        createOntologyItem "id28" "protein.synthesis.initiation" 1 "description28"
+        createOntologyItem "id29" "protein.synthesis.initiation" 1 "description29"
+        createOntologyItem "id30" "protein.synthesis" 0 "description30" //17
+        createOntologyItem "id31" "singletest" 1 "description31" //1
+    |]
+
+    let dataSplit = 
+        data
+        |> Seq.collect (splitMultipleAnnotationsBy ';')
+
+    let dataExtended = 
+        expandOntologyTree dataSplit
+
+    let enrichmentResult = 
+        calcOverEnrichmentIncludeFDR 1 (Some 0) (Some 0) dataExtended
+
+    [<Fact>]
+    let ``splitOntologyItems`` () =
+        let actual = dataSplit |> Seq.length
+        let expected = data.Length + 1 //first one is split into 2, all others remain the same
+        Assert.Equal<int>(expected, actual)
+
+    [<Fact>]
+    let ``expandOntologyTree`` () =
+        let actual = dataExtended |> Seq.length
+        let expected = 92 // 36 + 8 + 18 + 12 + 18
+        Assert.Equal<int>(expected, actual)
+
+    [<Fact>]
+    let ``ontologyEnrichment`` () =
+        // per bin one result
+        let numberOfBins_actual = enrichmentResult |> Seq.length
+        let numberOfBins_expected = 10
+        Assert.Equal<int>(numberOfBins_expected, numberOfBins_actual)
+        let bin1 = enrichmentResult |> Seq.find (fun x -> x.OntologyTerm = "PS.lightreaction.LHCII")
+        Assert.Equal<int>(11, bin1.NumberInBin)
+        Assert.Equal<int>(5, bin1.NumberOfDEsInBin)
+        Assert.Equal<int>(39, bin1.TotalNumberOfDE)
+        Assert.Equal<int>(92, bin1.TotalUniverse)
+        Assert.Equal<float>(0.5367813329, System.Math.Round(bin1.PValue, 10)) //https://systems.crump.ucla.edu/hypergeometric/index.php
+        let testbin = 
+            enrichmentResult |> Seq.find (fun x -> x.OntologyTerm = "singletest")
+        // test for a singleton bin of which valid p values exist
+        Assert.Equal<float>(0.4239130435, System.Math.Round(testbin.PValue, 10))