public double GetRankSumTestPvalue(Ms1Peak[] peaks, int envelopeSize)
{
if (PeakRanking == null)
{
return(1.0d);
}
// calculate ranksum test score
var ranksum = 0;
var nRankSum = 0;
for (var i = 0; i < envelopeSize; i++)
{
if (peaks[i] == null || !peaks[i].Active)
{
continue;
}
var localIndex = peaks[i].IndexInSpectrum - PeakStartIndex;
if (localIndex >= PeakCount || localIndex < 0)
{
continue;
}
ranksum += PeakRanking[localIndex];
nRankSum++;
}
var pvalue = FitScoreCalculator.GetRankSumPvalue(PeakCount, nRankSum, ranksum);
return(pvalue);
}
private double GetRankSumScore()
{
var rankSum = 0d;
var nMatchedIons = _prefixIonPeakIndex.Count + _suffixIonPeakIndex.Count;
var nObservedPeaks = _ms2Spec.Peaks.Length;
foreach (var peakIndex in _prefixIonPeakIndex)
{
rankSum += _peakRanking[peakIndex];
}
foreach (var peakIndex in _suffixIonPeakIndex)
{
rankSum += _peakRanking[peakIndex];
}
var pvalue = FitScoreCalculator.GetRankSumPvalue(nObservedPeaks, nMatchedIons, rankSum);
if (pvalue > 0)
{
return(-Math.Log(pvalue, 2));
}
return(50);
}
public IsotopeEnvelopeStatisticalInfo PreformStatisticalSignificanceTest(ObservedIsotopeEnvelope envelope)
{
int peakStartIndex;
Tuple <double, double> mzBoundary;
//var refPeak = envelope.Peaks[envelope.RefIsotopeInternalIndex];
var mostAbuMz = 0d;
var mostAbutPeakInternalIndex = envelope.TheoreticalEnvelope.IndexOrderByRanking[0];
if (envelope.Peaks[mostAbutPeakInternalIndex] != null)
{
mostAbuMz = envelope.Peaks[mostAbutPeakInternalIndex].Mz;
}
else
{
mostAbuMz = envelope.TheoreticalEnvelope.GetIsotopeMz(envelope.Charge, mostAbutPeakInternalIndex);
}
var rankings = GetLocalRankings(mostAbuMz, out peakStartIndex, out mzBoundary);
// smallest delta_mz = 0.01 (th) ?
var ret = new IsotopeEnvelopeStatisticalInfo
{
LocalMzStart = mzBoundary.Item1,
LocalMzEnd = mzBoundary.Item2,
NumberOfLocalPeaks = rankings.Length,
NumberOfPossiblePeaks = (int)Math.Ceiling(100 * (mzBoundary.Item2 - mzBoundary.Item1)),
NumberOfIsotopePeaks = envelope.Size,
};
// calculate ranksum test score
var ranksum = 0;
var nRankSum = 0;
for (var i = 0; i < envelope.Size; i++)
{
if (envelope.Peaks[i] == null || !envelope.Peaks[i].Active)
{
continue;
}
ret.NumberOfMatchedIsotopePeaks++;
//if (isotopeList[i].Ratio > RelativeIntesnityThresholdForRankSum)
//{
var localIndex = envelope.Peaks[i].IndexInSpectrum - peakStartIndex;
if (localIndex >= rankings.Length || localIndex < 0)
{
continue;
}
ranksum += rankings[localIndex];
nRankSum++;
//}
}
var pvalue = FitScoreCalculator.GetRankSumPvalue(ret.NumberOfLocalPeaks, nRankSum, ranksum);
ret.RankSumScore = (pvalue > 0) ? -Math.Log(pvalue, 2) : 50;
// calculate poisson test score
var n = ret.NumberOfPossiblePeaks;
var k = ret.NumberOfIsotopePeaks; // # of theretical isotope ions of the mass within the local window
var n1 = ret.NumberOfLocalPeaks; // # of detected ions within the local window
var k1 = ret.NumberOfMatchedIsotopePeaks; // # of matched ions generating isotope envelope profile
var lambda = ((double)n1 / (double)n) * k;
pvalue = 1 - Poisson.CDF(lambda, k1);
ret.PoissonScore = (pvalue > 0) ? -Math.Log(pvalue, 2) : 50;
return(ret);
}