private List <double> PonderatedRatio(PeptideResult pep)
{
List <double> ratios = new List <double>();
foreach (SQTScan s in pep.MyScans)
{
double weightSum = 0;
double numerator = 0;
foreach (List <double> quants in s.Quantitation)
{
double w = quants[0] + quants[1];
numerator += ((quants[0] / quants[1]) * w);
weightSum += w;
ReportItem ri = new ReportItem(s.FileName, s.ScanNumber, s.ChargeState, quants[0], quants[1], Math.Log(quants[0] / quants[1], 2), s.PeptideSequence);
reportItems.Add(ri);
}
ratios.Add(numerator / weightSum);
}
return(ratios);
}
private static List <double> ExtractValues(PeptideResult pep, int dim)
{
List <double> q1 = (from sqts in pep.MyScans
from quants in sqts.Quantitation
select quants[dim]).ToList();
q1.RemoveAll(a => double.IsInfinity(a) || double.IsNaN(a));
return(q1);
}
private void dataGridPeptideSelector_SelectedCellsChanged(object sender, SelectedCellsChangedEventArgs e)
{
try
{
PeptideResult pepR = (PeptideResult)dataGridPeptideSelector.SelectedItem;
dataGridPeptides.ItemsSource = pepR.MyScans;
}
catch (Exception e4)
{
Console.WriteLine("Couldn't plot protein : " + e4.Message);
}
}
private void CorrectIsotopic(PeptideResult pep)
{
int result = (int)Math.Round((pep.MyScans[0].MeasuredMH - pep.MyScans[0].TheoreticalMH), 0);
List <double> signal = isotopicSignalGenerator.GetSignal(15, pep.MyScans[0].MeasuredMH, 0);
foreach (SQTScan s in pep.MyScans)
{
int noMods = Regex.Matches(s.PeptideSequenceCleaned, Regex.Escape("(")).Count;
foreach (List <double> q in s.Quantitation)
{
}
}
Console.Write(".");
//Count how many deltas are there in the peptide
}
private static List <double> ExtractRatios(PeptideResult pep)
{
List <double> q1 = (from sqts in pep.MyScans
from quants in sqts.Quantitation
select Math.Log(quants[0] / quants[1], 2)).ToList();
q1.RemoveAll(a => double.IsInfinity(a) || double.IsNaN(a));
for (int i = 0; i < q1.Count; i++)
{
if (q1[i] > 15)
{
q1[i] = 15;
}
else if (q1[i] < -15)
{
q1[i] = -15;
}
}
return(q1);
}
private static PeptideLabelRatio FindPeptideLabelRatio(PeptideResult peptideResult, IsotopeLabelType labelType, IsotopeLabelType standardType)
{
return(peptideResult.ChromInfo.LabelRatios.FirstOrDefault(
labelRatio => ReferenceEquals(labelType, labelRatio.LabelType) &&
ReferenceEquals(standardType, labelRatio.StandardType)));
}
private void Old()
{
//Load the SEPro files;
PatternTools.LstSquQuadRegr lstsqr = new PatternTools.LstSquQuadRegr();
Console.WriteLine("Loading SEPro1");
ResultPackage sepro1 = ResultPackage.Load(textBoxSEProL1.Text);
Console.WriteLine("Loading SEPro2");
ResultPackage sepro2 = ResultPackage.Load(textBoxSEProL2.Text);
//Generate a list of all clean peptide sequences
List <string> cleanPeptideSequences = sepro1.AllPeptideSequences;
cleanPeptideSequences.AddRange(sepro2.AllPeptideSequences);
cleanPeptideSequences = cleanPeptideSequences.Distinct().ToList();
Console.WriteLine(" Peptides loaded: " + cleanPeptideSequences.Count);
//First lets normalize
List <GraphData> theData = new List <GraphData>(cleanPeptideSequences.Count);
double totalXP1 = 0;
double totalXP2 = 0;
double totalYP1 = 0;
double totalYP2 = 0;
foreach (string peptide in cleanPeptideSequences)
{
PeptideResult pep1 = sepro1.MyProteins.MyPeptideList.Find(a => a.CleanedPeptideSequence.Equals(peptide));
PeptideResult pep2 = sepro2.MyProteins.MyPeptideList.Find(a => a.CleanedPeptideSequence.Equals(peptide));
CorrectIsotopic(pep1);
CorrectIsotopic(pep2);
if (pep1 == null || pep2 == null)
{
continue;
}
totalXP1 += ExtractValues(pep1, 0).Sum();
totalYP1 += ExtractValues(pep1, 1).Sum();
totalXP2 += ExtractValues(pep2, 0).Sum();
totalYP2 += ExtractValues(pep2, 1).Sum();
}
foreach (string peptide in cleanPeptideSequences)
{
PeptideResult pep1 = sepro1.MyProteins.MyPeptideList.Find(a => a.CleanedPeptideSequence.Equals(peptide));
PeptideResult pep2 = sepro2.MyProteins.MyPeptideList.Find(a => a.CleanedPeptideSequence.Equals(peptide));
if (pep1 == null || pep2 == null)
{
continue;
}
List <double> beforeNorm = ExtractRatios(pep1);
if (pep1 == null || pep2 == null)
{
continue;
}
foreach (SQTScan scan in pep1.MyScans)
{
for (int i = 0; i < scan.Quantitation.Count; i++)
{
scan.Quantitation[i][0] /= totalXP1;
scan.Quantitation[i][1] /= totalYP1;
}
}
foreach (SQTScan scan in pep2.MyScans)
{
for (int i = 0; i < scan.Quantitation.Count; i++)
{
scan.Quantitation[i][0] /= totalXP2;
scan.Quantitation[i][1] /= totalYP2;
}
}
List <double> afterNorm = ExtractRatios(pep1);
}
//finished Normalizing
foreach (string peptide in cleanPeptideSequences)
{
PeptideResult pep1 = sepro1.MyProteins.MyPeptideList.Find(a => a.CleanedPeptideSequence.Equals(peptide));
PeptideResult pep2 = sepro2.MyProteins.MyPeptideList.Find(a => a.CleanedPeptideSequence.Equals(peptide));
if (pep1 == null || pep2 == null)
{
continue;
}
List <double> q1 = ExtractRatios(pep1);
List <double> q2 = ExtractRatios(pep2);
if (q1.Count == 0 || q2.Count == 0)
{
//Most likely we are here because this peptide is a false positive as it has two different labels in it.
Console.Write("x");
continue;
}
double x = 0;
if (q1.Count > 0)
{
x = q1.Average();
}
//x = q1[0];
double y = 0;
if (q2.Count > 0)
{
y = q2.Average();
}
//y = q2[0];
theData.Add(new GraphData(x, y));
Console.Write(".");
}
//And now, print the data to the graph
chart1.Series[0].Points.Clear();
chart1.ChartAreas[0].AxisX.Crossing = 0;
chart1.ChartAreas[0].AxisY.Crossing = 0;
chart1.ChartAreas[0].AxisY.IsStartedFromZero = true;
chart1.ChartAreas[0].AxisX.IsStartedFromZero = true;
foreach (GraphData g in theData)
{
lstsqr.AddPoints(g.X, g.Y);
chart1.Series[0].Points.AddXY(g.X, g.Y);
}
//Finally, update the labels
labelL1.Text = Math.Round(theData.Average(a => a.X), 3).ToString() + " +- " + Math.Round(PatternTools.pTools.Stdev(theData.Select(a => a.X).ToList(), true), 3);
labelL2.Text = Math.Round(theData.Average(a => a.Y), 3).ToString() + " +- " + Math.Round(PatternTools.pTools.Stdev(theData.Select(a => a.Y).ToList(), true), 3);
//labelRSquared.Text = Math.Round(lstsqr.rSquare(),3).ToString();
//labelRegressorEquation.Text = "y = " + Math.Round(lstsqr.aTerm(),2) + " x^2 + " + Math.Round(lstsqr.bTerm(),2) + " x + " + Math.Round(lstsqr.cTerm(),2);
dataGridViewPoints.DataSource = theData;
}