public void CompareAveragingWithMSstats()
{
var srmDocument = LoadRatPlasmaDocument();
var documentContainer = new MemoryDocumentContainer();
documentContainer.SetDocument(documentContainer.Document, srmDocument);
GroupComparisonModel model = new GroupComparisonModel(documentContainer, null);
model.GroupComparisonDef = GroupComparisonDef.EMPTY.ChangeControlAnnotation("Condition")
.ChangeControlValue("Healthy")
.ChangeIdentityAnnotation("BioReplicate")
.ChangeSummarizationMethod(SummarizationMethod.AVERAGING)
.ChangePerProtein(false);
var expectedValues = MsStatsTestUtil.ReadExpectedResults(typeof(MSstatsAveragingTest),
"RatPlasmaTestingResult.csv");
var groupComparer = new GroupComparer(model.GroupComparisonDef, srmDocument, new QrFactorizationCache());
foreach (var protein in srmDocument.PeptideGroups)
{
foreach (var peptide in protein.Peptides)
{
var result = groupComparer.CalculateFoldChange(new GroupComparisonSelector(protein, peptide, IsotopeLabelType.light, null, new GroupIdentifier("Diseased")), null);
var expectedResult = expectedValues[peptide.Peptide.Sequence];
Assert.AreEqual(expectedResult.EstimatedValue, result.LinearFitResult.EstimatedValue,
(expectedResult.StandardError + result.LinearFitResult.StandardError) * 2, peptide.Peptide.Sequence);
}
}
}
public void TestProteinAbundance()
{
var srmDocument = LoadRatPlasmaDocument();
var documentContainer = new MemoryDocumentContainer();
documentContainer.SetDocument(srmDocument, documentContainer.Document);
var skylineDataSchema = new SkylineDataSchema(documentContainer, DataSchemaLocalizer.INVARIANT);
GroupComparisonModel model = new GroupComparisonModel(documentContainer, null);
model.GroupComparisonDef = GroupComparisonDef.EMPTY.ChangeControlAnnotation("Condition")
.ChangeControlValue("Healthy")
.ChangeSummarizationMethod(SummarizationMethod.AVERAGING)
.ChangePerProtein(true);
var groupComparer = new GroupComparer(model.GroupComparisonDef, srmDocument, new QrFactorizationCache());
foreach (var moleculeGroup in srmDocument.MoleculeGroups)
{
if (moleculeGroup.Molecules.Any(mol => null != mol.GlobalStandardType))
{
continue;
}
var foldChangeResult = groupComparer.CalculateFoldChange(new GroupComparisonSelector(moleculeGroup, null, IsotopeLabelType.light, null, new GroupIdentifier("Diseased")), null);
var xValues = new List <double>();
var yValues = new List <double>();
var protein = new Protein(skylineDataSchema, new IdentityPath(moleculeGroup.PeptideGroup));
foreach (var proteinResult in protein.Results.Values)
{
var abundance = proteinResult.Abundance;
if (!abundance.HasValue)
{
continue;
}
var condition = proteinResult.Replicate.ChromatogramSet.Annotations.GetAnnotation("Condition");
if (condition == "Healthy")
{
xValues.Add(0);
}
else if (condition == "Diseased")
{
xValues.Add(1);
}
yValues.Add(Math.Log(abundance.Value));
}
Assert.AreEqual(xValues.Count, foldChangeResult.ReplicateCount);
if (!xValues.Any())
{
continue;
}
var yStatistics = new Statistics(yValues);
var xStatistics = new Statistics(xValues);
var slope = yStatistics.Slope(xStatistics);
var actualFoldChange = Math.Exp(slope);
var expectedFoldChange = Math.Pow(2.0, foldChangeResult.LinearFitResult.EstimatedValue);
AssertEx.AreEqual(expectedFoldChange, actualFoldChange, .01);
}
}
public EditGroupComparisonDlg(GroupComparisonModel groupComparisonModel)
{
InitializeComponent();
Icon = Resources.Skyline;
GroupComparisonModel = groupComparisonModel;
GroupComparisonModel.AddModelChanged(this, OnModelChanged);
Height -= panelAdvanced.Height;
panelAdvanced.Visible = false;
}
private void OnModelChanged(GroupComparisonModel model)
{
if (_inChangeSettings)
{
return;
}
try
{
_inChangeSettings = true;
UpdateSettings();
}
finally
{
_inChangeSettings = false;
}
}
public static void ChangeGroupComparisonDef(bool pushChangesToDocument, GroupComparisonModel model, GroupComparisonDef groupDef)
{
if (pushChangesToDocument)
{
Program.MainWindow.ModifyDocument(
GroupComparisonStrings.GroupComparisonSettingsForm_GroupComparisonDef_Change_Group_Comparison,
doc => model.ApplyChangesToDocument(doc, groupDef)
);
Settings.Default.GroupComparisonDefList.Add(groupDef);
}
else
{
model.GroupComparisonDef = groupDef;
}
}
public GroupComparisonRefinementData(SrmDocument document, double adjustedPValCutoff,
double foldChangeCutoff, int?msLevel, List <GroupComparisonDef> groupComparisonDefs,
SrmSettingsChangeMonitor progressMonitor)
{
_progressMonitor = progressMonitor;
_foldChangeCutoff = foldChangeCutoff;
_adjustedPValCutoff = adjustedPValCutoff;
if (msLevel.HasValue)
{
_msLevel = msLevel.Value;
}
else
{
_msLevel = document.PeptideTransitions.Any(t => !t.IsMs1) ? 2 : 1;
}
Data = new List <List <GroupComparisonRow> >();
foreach (var groupComparisonDef in groupComparisonDefs)
{
var groupComparer = new GroupComparer(groupComparisonDef, document, _qrFactorizationCache);
var results = GroupComparisonModel.ComputeResults(groupComparer, document, null, null, progressMonitor);
var adjustedPValues = PValues.AdjustPValues(results.Select(
row => row.LinearFitResult.PValue)).ToArray();
var foldChangeList = new List <GroupComparisonRow>();
for (int iRow = 0; iRow < results.Count; iRow++)
{
var resultRow = results[iRow];
FoldChangeResult foldChangeResult = new FoldChangeResult(groupComparisonDef.ConfidenceLevel,
adjustedPValues[iRow], resultRow.LinearFitResult, double.NaN);
foldChangeList.Add(new GroupComparisonRow(resultRow.Selector.Protein, resultRow.Selector.Peptide,
resultRow.Selector.MsLevel,
foldChangeResult));
}
Data.Add(foldChangeList);
}
}
public FoldChangeBindingSource(GroupComparisonModel groupComparisonModel)
{
_container = new Container();
GroupComparisonModel = groupComparisonModel;
_taskScheduler = TaskScheduler.FromCurrentSynchronizationContext();
}
public FoldChangeBindingSource(GroupComparisonModel groupComparisonModel)
{
_container = new Container();
GroupComparisonModel = groupComparisonModel;
_taskScheduler = new EventTaskScheduler();
}
protected BaseGroupComparisonSettings(GroupComparisonModel groupComparisonModel)
{
GroupComparisonModel = groupComparisonModel;
GroupComparisonModel.AddModelChanged(this, OnModelChanged);
}
