public GroupComparisonRow(PeptideGroupDocNode protein, PeptideDocNode peptide, int?msLevel, FoldChangeResult result)
{
Protein = protein;
Peptide = peptide;
MsLevel = msLevel;
FoldChangeResult = result;
}
public FoldChangeRow(Protein protein, Model.Databinding.Entities.Peptide peptide, IsotopeLabelType labelType,
int?msLevel, GroupIdentifier group, int replicateCount, FoldChangeResult foldChangeResult, IDictionary <Replicate, ReplicateRow> replicateResults)
: base(protein, peptide, labelType, msLevel, replicateResults)
{
ReplicateCount = replicateCount;
FoldChangeResult = foldChangeResult;
Group = group;
}
public FoldChangeRow(Protein protein, Model.Databinding.Entities.Peptide peptide, IsotopeLabelType labelType,
int?msLevel, GroupIdentifier group, int replicateCount, FoldChangeResult foldChangeResult)
{
Protein = protein;
Peptide = peptide;
IsotopeLabelType = labelType;
MsLevel = msLevel;
ReplicateCount = replicateCount;
FoldChangeResult = foldChangeResult;
Group = group;
}
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 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);
}
