public void TestSimpleAdjustPValues()
{
var input = new[] { .005, .02, .25 };
var expected = new[] { .015, .030, .250 };
var actual = PValues.AdjustPValues(input);
CollectionAssert.AreEqual(expected, actual);
}
private void UpdateResults()
{
var results = GroupComparisonModel.Results;
var rows = new List <FoldChangeRow>();
if (null != results)
{
Dictionary <int, double> criticalValuesByDegreesOfFreedom = new Dictionary <int, double>();
var groupComparisonDef = results.GroupComparer.ComparisonDef;
var adjustedPValues = PValues.AdjustPValues(results.ResultRows.Select(
row => row.LinearFitResult.PValue)).ToArray();
for (int iRow = 0; iRow < results.ResultRows.Count; iRow++)
{
var resultRow = results.ResultRows[iRow];
var protein = new Protein(_skylineDataSchema, new IdentityPath(resultRow.Selector.Protein.Id));
Model.Databinding.Entities.Peptide peptide = null;
if (null != resultRow.Selector.Peptide)
{
peptide = new Model.Databinding.Entities.Peptide(_skylineDataSchema,
new IdentityPath(protein.IdentityPath, resultRow.Selector.Peptide.Id));
}
double criticalValue;
if (!criticalValuesByDegreesOfFreedom.TryGetValue(resultRow.LinearFitResult.DegreesOfFreedom,
out criticalValue))
{
criticalValue = FoldChangeResult.GetCriticalValue(groupComparisonDef.ConfidenceLevel,
resultRow.LinearFitResult.DegreesOfFreedom);
criticalValuesByDegreesOfFreedom.Add(resultRow.LinearFitResult.DegreesOfFreedom, criticalValue);
}
FoldChangeResult foldChangeResult = new FoldChangeResult(groupComparisonDef.ConfidenceLevel,
adjustedPValues[iRow], resultRow.LinearFitResult, criticalValue);
rows.Add(new FoldChangeRow(protein, peptide, resultRow.Selector.LabelType,
resultRow.Selector.MsLevel, resultRow.Selector.GroupIdentifier, resultRow.ReplicateCount, foldChangeResult));
}
}
var defaultViewSpec = GetDefaultViewSpec(rows);
if (!Equals(defaultViewSpec, ViewContext.BuiltInViews.First()))
{
var viewInfo = new ViewInfo(_skylineDataSchema, typeof(FoldChangeRow), defaultViewSpec).ChangeViewGroup(ViewGroup.BUILT_IN);
ViewContext.SetRowSources(new[]
{
new RowSourceInfo(new StaticRowSource(rows), viewInfo)
});
if (null != _bindingListSource.ViewSpec && _bindingListSource.ViewSpec.Name == defaultViewSpec.Name &&
!_bindingListSource.ViewSpec.Equals(defaultViewSpec))
{
_bindingListSource.SetView(viewInfo, new StaticRowSource(rows));
}
}
_bindingListSource.RowSource = new StaticRowSource(rows);
}
public override string GetCommandLineArguments()
{
StringBuilder arguments = new StringBuilder();
string formattedPValues = PValues.Replace(" ", "");
//need to escape the < symbol on windows (linux ok)
if (RuntimeInformation.IsOSPlatform(OSPlatform.Windows))
{
formattedPValues = formattedPValues.Replace("<", "^<");
}
arguments.Append(" " + formattedPValues); //4
arguments.Append(" " + SelectedTest); //5
arguments.Append(" " + Significance); //6
return(arguments.ToString().Trim());
}
public void TestAdjustListOfPValues()
{
var input = new[]
{
0, 7.2867665485711353e-01, 1.1395351451692903e-04, 0, 0,
0, 0, 5.7295134488581922e-03, 3.6202576492172511e-08, 0,
6.6968629752750530e-08, 0, 0, 0, 0,
0, 0, 0, 0, 0,
2.6345568091021576e-01, 0, 1.1774885228897247e-02, 2.0858033300541479e-08, 0,
0, 2.3421400293432981e-05, 0, 0, 0,
0, 3.3684388611732174e-10, 0, 2.0239094797527057e-01, 0,
7.9936057773011271e-15, 4.4724224323999806e-12, 0, 0, 4.0897231039323190e-01,
0, 7.5570363823769249e-03, 0, 4.2761477929438962e-01, 4.5888446988493703e-02,
9.7037489155127332e-11, 2.0262598487530425e-05, 0
};
var expected = new[]
{
0, 7.2867665485711353e-01, 1.4025047940545112e-04, 0, 0,
0, 0, 6.8754161386298304e-03, 4.9649247760693727e-08, 0,
8.9291506337000698e-08, 0, 0, 0, 0,
0, 0, 0, 0, 0,
2.8101939297089679e-01, 0, 1.3457011690168282e-02, 2.9446635247823267e-08, 0,
0, 2.9584926686441660e-05, 0, 0, 0,
0, 4.8995474344337708e-10, 0, 2.2079012506393153e-01, 0,
1.2789769243681804e-14, 6.9250411856515830e-12, 0, 0, 4.2675371519293764e-01,
0, 8.8472621061973754e-03, 0, 4.3671296608788723e-01, 5.1224312917388319e-02,
1.4555623373269100e-10, 2.6286614254093528e-05, 0,
};
var actual = PValues.AdjustPValues(input);
for (int i = 0; i < expected.Length; i++)
{
if (expected[i] == 0)
{
Assert.AreEqual(expected[i], actual[i]);
}
else
{
Assert.AreEqual(expected[i], actual[i], expected[i] / 1E8);
}
}
}
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);
}
}
private void UpdateResults()
{
var results = GroupComparisonModel.Results;
var rows = new List <FoldChangeRow>();
if (null != results)
{
var controlGroupIdentifier =
GroupComparisonModel.GroupComparisonDef.GetControlGroupIdentifier(_skylineDataSchema.Document
.Settings);
Dictionary <int, double> criticalValuesByDegreesOfFreedom = new Dictionary <int, double>();
var groupComparisonDef = results.GroupComparer.ComparisonDef;
var adjustedPValues = PValues.AdjustPValues(results.ResultRows.Select(
row => row.LinearFitResult.PValue)).ToArray();
for (int iRow = 0; iRow < results.ResultRows.Count; iRow++)
{
var resultRow = results.ResultRows[iRow];
var protein = new Protein(_skylineDataSchema, new IdentityPath(resultRow.Selector.Protein.Id));
Model.Databinding.Entities.Peptide peptide = null;
if (null != resultRow.Selector.Peptide)
{
peptide = new Model.Databinding.Entities.Peptide(_skylineDataSchema,
new IdentityPath(protein.IdentityPath, resultRow.Selector.Peptide.Id));
}
double criticalValue;
if (!criticalValuesByDegreesOfFreedom.TryGetValue(resultRow.LinearFitResult.DegreesOfFreedom,
out criticalValue))
{
criticalValue = FoldChangeResult.GetCriticalValue(groupComparisonDef.ConfidenceLevel,
resultRow.LinearFitResult.DegreesOfFreedom);
criticalValuesByDegreesOfFreedom.Add(resultRow.LinearFitResult.DegreesOfFreedom, criticalValue);
}
FoldChangeResult foldChangeResult = new FoldChangeResult(groupComparisonDef.ConfidenceLevel,
adjustedPValues[iRow], resultRow.LinearFitResult, criticalValue);
var runAbundances = new Dictionary <Replicate, ReplicateRow>();
foreach (var runAbundance in resultRow.RunAbundances)
{
Replicate replicate = new Replicate(_skylineDataSchema, runAbundance.ReplicateIndex);
runAbundances.Add(replicate, new ReplicateRow(replicate, runAbundance.Control ?
controlGroupIdentifier : resultRow.Selector.GroupIdentifier
, runAbundance.BioReplicate, Math.Pow(2, runAbundance.Log2Abundance)));
}
rows.Add(new FoldChangeRow(protein, peptide, resultRow.Selector.LabelType,
resultRow.Selector.MsLevel, resultRow.Selector.GroupIdentifier, resultRow.ReplicateCount, foldChangeResult, runAbundances));
}
}
var detailRows = new List <FoldChangeDetailRow>();
foreach (var grouping in rows.ToLookup(row =>
Tuple.Create(row.Protein, row.Peptide, row.IsotopeLabelType, row.MsLevel)))
{
var foldChangeResults = grouping.ToDictionary(row => row.Group, row => row.FoldChangeResult);
var runAbundances = new Dictionary <Replicate, ReplicateRow>();
foreach (var abundance in grouping.SelectMany(row => row.ReplicateAbundances))
{
runAbundances[abundance.Key] = abundance.Value;
}
detailRows.Add(new FoldChangeDetailRow(grouping.Key.Item1, grouping.Key.Item2, grouping.Key.Item3, grouping.Key.Item4, foldChangeResults, runAbundances));
}
var defaultViewSpec = GetDefaultViewSpec(rows);
var clusteredViewSpec = GetClusteredViewSpec(defaultViewSpec);
var rowSourceInfos = new List <RowSourceInfo>()
{
new RowSourceInfo(new StaticRowSource(rows),
new ViewInfo(_skylineDataSchema, typeof(FoldChangeRow), defaultViewSpec).ChangeViewGroup(ViewGroup.BUILT_IN)),
new RowSourceInfo(new StaticRowSource(detailRows),
new ViewInfo(_skylineDataSchema, typeof(FoldChangeDetailRow), clusteredViewSpec).ChangeViewGroup(ViewGroup.BUILT_IN))
};
SetRowSourceInfos(rowSourceInfos);
}
protected override void BeforeTest(Commons.Spec.ExecutionModel.TestUnit test)
{
Value = new PValues();
Subject = new ReflectionProperties(Value);
}
