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);
}
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;
}
