private void ProcessPeptideQuantitationReport2()
{
KeyValuePair <List <FastaItem>, List <PepQuant> > kvp = UniQTools.ParsePeptideReport(peptideQuantitationReportFile);
//Some error checking
if (classLabels.Count > kvp.Value[0].MyQuants[0].MarkerIntensities.Count)
{
MessageBox.Show("Parameter Min no Quants per reading cannot be greater than number of channels specidied in the class menu.");
return;
}
if (classLabels.Count != kvp.Value[0].MyQuants[0].MarkerIntensities.Count)
{
MessageBox.Show("Make sure you properly labeled your class labels followed with spaces as they do not match those from the peptide quantitation report.");
return;
}
UniQTools.ScorePepQuants(classLabels, kvp.Value);
MyPeptides = kvp.Value;
MyFastaItems = kvp.Key;
protPepDict = new Dictionary <FastaItem, List <PepQuant> >();
//Parallel.ForEach(MyFastaItems, fi =>
foreach (FastaItem fi in MyFastaItems)
{
List <PepQuant> pepts = MyPeptides.FindAll(a => fi.Sequence.Contains(a.CleanPeptideSequence));
if (pepts.Count > 0)
{
protPepDict.Add(fi, pepts);
}
foreach (PepQuant pq in pepts)
{
pq.MappableProteins.Add(fi.SequenceIdentifier);
}
}
//);
return;
}
public void UpdateGUI()
{
//Lets take care of which peptides to consider in our analysis
if ((bool)CheckBoxConsiderOnlyUniquePeptides.IsChecked)
{
myPeptidesTMP = MyPeptides.FindAll(a => a.MappableProteins.Count == 1);
}
else
{
myPeptidesTMP = MyPeptides.FindAll(a => a.MappableProteins.Count > 0);
}
int removedFold = myPeptidesTMP.RemoveAll(a => Math.Abs(a.AVGLogFold) < Math.Round((double)DoubleUpDownPeptideLogFold.Value, 2));
///Need to fix here....
int removedProb1 = myPeptidesTMP.RemoveAll(a => (a.TTest > Math.Round((double)DoubleUpDownPeptidePValueCutoff.Value, 2)));
List <PepQuant> survival = MyPeptides.FindAll(a => !myPeptidesTMP.Exists(b => b.Sequence.Equals(a.Sequence)));
protPepDictTMP = new Dictionary <FastaItem, List <PepQuant> >();
//New way
foreach (FastaItem fi in MyFastaItems)
{
List <PepQuant> pepts = myPeptidesTMP.FindAll(a => a.MappableProteins.Contains(fi.SequenceIdentifier));
if (pepts.Count > 0)
{
protPepDictTMP.Add(fi, pepts);
}
}
try
{
var protDisplay = from kvp in protPepDictTMP
where kvp.Value.Count >= IntegerUpDown.Value
select new
{
ProtID = kvp.Key.SequenceIdentifier,
Daltons = Math.Round(kvp.Key.MonoisotopicMass, 2),
PeptideCount = kvp.Value.Count,
UniquePeptideCount = kvp.Value.Count(a => a.MappableProteins.Count == 1),
SpecCount = protPepDictTMP[kvp.Key].Sum(a => a.MyQuants.Count),
AvgLogFold = Math.Round(kvp.Value.Average(a => a.AVGLogFold), 3),
StouffersPValue = ProteinPValue(kvp.Value),
Coverage = GenerateMicroChart(kvp),
Description = kvp.Key.Description
};
int noProteins = protDisplay.Count();
LabelNoProteins.Content = noProteins;
if (noProteins == 0)
{
MessageBox.Show("No protein satisfies current constraints.");
return;
}
//Find out how many peptides and spec counts are there
List <PepQuant> validPepQuants = new List <PepQuant>();
if ((bool)CHeckBoxShowPeptidesOfFilteredProteinsOnly.IsChecked)
{
List <string> IDsProteinsDisplay = protDisplay.Select(a => a.ProtID).ToList();
foreach (string pID in IDsProteinsDisplay)
{
FastaItem fi = MyFastaItems.Find(a => a.SequenceIdentifier.Equals(pID));
validPepQuants.AddRange(protPepDictTMP[fi]);
}
validPepQuants = validPepQuants.Distinct().ToList();
}
else
{
validPepQuants = MyPeptides;
}
DataGridAllPeptidesView.ItemsSource = validPepQuants.Select
(a => new
{
Sequence = a.Sequence,
Binomial_PValue = Math.Round(a.BinomialProbability, 4),
Paired_TTest_Pvalue = Math.Round(a.TTest, 4),
AVGLogFold = Math.Round(a.AVGLogFold, 4),
Redundancy = a.MappableProteins.Count,
SpecCount = a.MyQuants.Count,
MissingValues = a.MissingValues,
MappableProts = string.Join(" ", (
from prot in protDisplay
where a.MappableProteins.Contains(prot.ProtID)
select "(" + prot.ProtID + "::" + prot.Description + ")").ToList()
)
}
);
LabelNoPeptides.Content = validPepQuants.Count();
LabelSpecCount.Content = validPepQuants.Sum(a => a.MyQuants.Count);
LabelAvgFilteredPepLogFold.Content = Math.Round(validPepQuants.Average(a => a.AVGLogFold), 3);
DataGridProteinView.ItemsSource = protDisplay;
myPeptidesTMP = validPepQuants;
double correctedP = PatternTools.pTools.BenjaminiHochbergFDR(0.01, protDisplay.Select(a => a.StouffersPValue).ToList(), false);
LabelCorrectedP.Content = correctedP;
LabelTotalPeptides.Content = MyPeptides.Count;
}
catch (Exception) { return; }
//Update the graphs
PlotQuants();
}
