public void ScoreFeatures(IProgressMonitor progressMonitor = null)
{
if (_features == null)
{
_features = Document.GetPeakFeatures(_calcs, progressMonitor);
}
if (ScoringModel == null)
{
return;
}
var bestTargetPvalues = new List <double>();
var targetIds = new List <PeakTransitionGroupIdKey>();
foreach (var transitionGroupFeatures in _features)
{
var mProphetScoresGroup = new List <double>();
foreach (var peakGroupFeatures in transitionGroupFeatures.PeakGroupFeatures)
{
mProphetScoresGroup.Add(ScoringModel.Score(peakGroupFeatures.Features));
}
var pValuesGroup = mProphetScoresGroup.Select(score => 1 - Statistics.PNorm(score)).ToList();
int bestIndex = mProphetScoresGroup.IndexOf(mProphetScoresGroup.Max());
double bestPvalue = pValuesGroup[bestIndex];
var featureStats = new PeakFeatureStatistics(transitionGroupFeatures, mProphetScoresGroup, pValuesGroup, bestIndex, null);
_featureDictionary.Add(transitionGroupFeatures.Id.Key, featureStats);
if (!transitionGroupFeatures.Id.NodePep.IsDecoy)
{
bestTargetPvalues.Add(bestPvalue);
targetIds.Add(transitionGroupFeatures.Id.Key);
}
}
_qValues = new Statistics(bestTargetPvalues).Qvalues(MProphetPeakScoringModel.DEFAULT_R_LAMBDA, MProphetPeakScoringModel.PI_ZERO_MIN).ToList();
for (int i = 0; i < _qValues.Count; ++i)
{
var newFeatureStats = _featureDictionary[targetIds[i]].SetQValue(_qValues[i]);
_featureDictionary[targetIds[i]] = newFeatureStats;
}
}
public void ScoreFeatures(IProgressMonitor progressMonitor = null, bool releaseRawFeatures = false, TextWriter output = null)
{
if (_features == null)
{
_features = Document.GetPeakFeatures(_calcs, progressMonitor);
}
if (ScoringModel == null)
{
return;
}
var bestTargetPvalues = new List <double>(_features.TargetCount);
var targetIds = new List <PeakTransitionGroupIdKey>(_features.TargetCount);
foreach (var transitionGroupFeatures in _features.Features)
{
int bestIndex = 0;
float bestScore = float.MinValue;
float bestPvalue = float.NaN;
var peakGroupFeatures = transitionGroupFeatures.PeakGroupFeatures;
IList <float> mProphetScoresGroup = null, pvalues = null;
if (!releaseRawFeatures)
{
mProphetScoresGroup = new float[peakGroupFeatures.Count];
}
if (!releaseRawFeatures)
{
pvalues = new float[peakGroupFeatures.Count];
}
for (int i = 0; i < peakGroupFeatures.Count; i++)
{
double score = ScoringModel.Score(peakGroupFeatures[i].Features);
if (double.IsNaN(bestScore) || score > bestScore)
{
bestIndex = i;
bestScore = (float)score;
bestPvalue = (float)(1 - Statistics.PNorm(score));
}
if (mProphetScoresGroup != null)
{
mProphetScoresGroup[i] = (float)score;
}
if (pvalues != null)
{
pvalues[i] = (float)(1 - Statistics.PNorm(score));
}
}
if (bestScore == float.MinValue)
{
bestScore = float.NaN;
}
var featureStats = new PeakFeatureStatistics(transitionGroupFeatures,
mProphetScoresGroup, pvalues, bestIndex, bestScore, null);
_featureDictionary.Add(transitionGroupFeatures.Key, featureStats);
if (!transitionGroupFeatures.IsDecoy)
{
bestTargetPvalues.Add(bestPvalue);
targetIds.Add(transitionGroupFeatures.Key);
}
}
_qValues = new Statistics(bestTargetPvalues).Qvalues(MProphetPeakScoringModel.DEFAULT_R_LAMBDA, MProphetPeakScoringModel.PI_ZERO_MIN);
for (int i = 0; i < _qValues.Length; ++i)
{
_featureDictionary[targetIds[i]].QValue = (float)_qValues[i];
}
if (releaseRawFeatures)
{
_features = null; // Done with this memory
}
}
public void ScoreFeatures(IProgressMonitor progressMonitor = null)
{
if (_features == null)
{
_features = Document.GetPeakFeatures(_calcs, progressMonitor);
}
if (ScoringModel == null)
return;
var bestTargetPvalues = new List<double>();
var targetIds = new List<PeakTransitionGroupIdKey>();
foreach (var transitionGroupFeatures in _features)
{
var mProphetScoresGroup = new List<double>();
foreach (var peakGroupFeatures in transitionGroupFeatures.PeakGroupFeatures)
{
mProphetScoresGroup.Add(ScoringModel.Score(peakGroupFeatures.Features));
}
var pValuesGroup = mProphetScoresGroup.Select(score => 1 - Statistics.PNorm(score)).ToList();
int bestIndex = mProphetScoresGroup.IndexOf(mProphetScoresGroup.Max());
double bestPvalue = pValuesGroup[bestIndex];
var featureStats = new PeakFeatureStatistics(transitionGroupFeatures, mProphetScoresGroup, pValuesGroup, bestIndex, null);
_featureDictionary.Add(transitionGroupFeatures.Id.Key, featureStats);
if (!transitionGroupFeatures.Id.NodePep.IsDecoy)
{
bestTargetPvalues.Add(bestPvalue);
targetIds.Add(transitionGroupFeatures.Id.Key);
}
}
_qValues = new Statistics(bestTargetPvalues).Qvalues(MProphetPeakScoringModel.DEFAULT_R_LAMBDA, MProphetPeakScoringModel.PI_ZERO_MIN).ToList();
for (int i = 0; i < _qValues.Count; ++i)
{
var newFeatureStats = _featureDictionary[targetIds[i]].SetQValue(_qValues[i]);
_featureDictionary[targetIds[i]] = newFeatureStats;
}
}
