public static double GetPValue(PSM psm, Tolerance prod_tolerance, double cutoff)
{
// Get the width of the product ion tolerance at the isolation mz;
double productToleranceWidth = prod_tolerance.GetRange(psm.IsolationMZ).Width;
double cutoffThreshold = psm.Spectrum.GetBasePeakIntensity()*cutoff;
return Math.Min(1.0, psm.Spectrum.Count(peak => peak.Intensity >= cutoffThreshold)*2*productToleranceWidth/psm.ScanWidth);
}
public Lotor(string rawFileDirectory, string inputcsvFile, string outputDirectory, List<Modification> fixedModifications, List<Modification> quantifiedModifications, Tolerance prod_Tolerance, int scoreCutoff, bool separateGroups, double productThreshold,bool ignoreCTerminal,bool reduceSites, FragmentTypes fragType, bool phosphoNeutralLoss = false)
{
_rawFileDirectory = rawFileDirectory;
_csvFile = inputcsvFile;
_outputDirectory = outputDirectory;
_fixedModifications = fixedModifications;
FixedModifications = fixedModifications.OfType<IMass>().ToList();
QuantifiedModifications = quantifiedModifications;
_prodTolerance = prod_Tolerance;
_deltaScoreCutoff = scoreCutoff;
_separateProteinGroups = separateGroups;
_productThreshold = productThreshold;
_fragType = fragType;
_ignoreCTerminal = ignoreCTerminal;
_reduceSites = reduceSites;
//LocalizedHit.AScoreThreshold = ascore_threshold;
LocalizedHit.ScoreThreshold = scoreCutoff;
_phosphoNeutralLoss = phosphoNeutralLoss;
}
public TagQuant(string outputDirectory, string rawFileDirectory, IEnumerable<string> inputFiles,
IEnumerable<TagInformation> tags, Tolerance itTolerance, Tolerance ftTolerance, bool isMS3Quant = false,
int etdQuantPosition = 0, bool nosiebasecap = false, bool isETDQuantified = true, bool calculatePurity = false)
{
RawFileDirectory = rawFileDirectory;
OutputDirectory = outputDirectory;
UsedTags = new SortedList<double, TagInformation>(tags.ToDictionary(t => t.MassCAD));
InputFiles = inputFiles.ToList();
NoisebandCap = nosiebasecap;
DontQuantifyETD = isETDQuantified;
MS3Quant = isMS3Quant;
CalculatePurity = calculatePurity;
ItMassTolerance = itTolerance;
FtMassTolerance = ftTolerance;
ETDQuantPosition = etdQuantPosition;
logWriter = new StreamWriter(Path.Combine(outputDirectory, "tagquant_log.txt"));
logWriter.AutoFlush = true;
RawFiles =
Directory.EnumerateFiles(rawFileDirectory, "*.raw")
.ToDictionary(file => Path.GetFileNameWithoutExtension(file), file => new ThermoRawFile(file));
}
private List<LocalizedHit> CalculateBestIsoforms(List<PSM> psms, FragmentTypes fragType, Tolerance prod_tolerance, double productThreshold, bool phosphoNeutralLosses)
{
Log("Localizing Best Isoforms...");
int totalisofromscount = 0;
int count = 0;
int psm_count = 0;
int localized_psm = 0;
List<LocalizedHit> hits = new List<LocalizedHit>();
foreach (PSM psm in psms)
{
psm_count++;
count++;
// Generate all the isoforms for the PSM
int isoformCount = psm.GenerateIsoforms(_ignoreCTerminal);
if(isoformCount == 0)
continue;
totalisofromscount += isoformCount;
// Calculate the probability of success for random matches
//double pvalue = GetPValue(psm, prod_tolerance, productThreshold);
// Match all the isoforms to the spectrum and log the results
psm.MatchIsofroms(fragType, prod_tolerance, productThreshold, phosphoNeutralLosses, 1);
// Perform the localization for all combinations of isoforms
//double[,] res = psm.Calc(pvalue);
Tuple<int, int, double> scores = LocalizedIsoformSimple(psm);
// Check if the localization is above some threshold
//Tuple<int, int, double> scores = LocalizedIsoform(res);
int bestIsoform = scores.Item1;
int secondBestIsoform = scores.Item2;
double ascore = scores.Item3;
//int numSDFs = psm.NumSiteDeterminingFragments[bestIsoform, secondBestIsoform];
List<PeptideIsoform> isoforms = psm.PeptideIsoforms.ToList();
//LocalizedHit hit = new LocalizedHit(psm, isoforms[bestIsoform], isoforms[secondBestIsoform], numSDFs,
// psm.BestSiteDeterminingFragments[bestIsoform, secondBestIsoform],
// psm.BestSiteDeterminingFragments[secondBestIsoform, bestIsoform], pvalue, ascore);
LocalizedHit hit = new LocalizedHit(psm, isoforms[bestIsoform], isoforms[secondBestIsoform], 0,
0,
0, 0, ascore);
hits.Add(hit);
if (hit.IsLocalized)
{
localized_psm++;
}
psm.PeptideIsoforms.Clear();
// Progress Bar Stuff
if (count <= 50)
continue;
count = 0;
ProgressUpdate((double)psm_count / psms.Count);
}
ProgressUpdate(1.0);
Log(string.Format("Total Number of Possible Isoforms Considered: {0:N0}",totalisofromscount));
Log(string.Format("Total Number of PSMs Considered: {0:N0}", psm_count));
Log(string.Format("Total Number of PSMs Localized: {0:N0} ({1:00.00}%)", localized_psm, localized_psm * 100 / psm_count));
ProgressUpdate(0);
return hits;
}
/// <summary>
/// Creates a range around some mean value with a specified tolerance.
/// <para>
/// i.e. 10 ppm at 500 would give you 499.9975 - 500.0025
/// which has a width of 0.005. Converting back to ppm
/// (1e6) *0.005 / 500 = 10 ppm.
/// </para>
/// <para>
/// The difference from the mean value to an boundary is exactly
/// half the tolerance you specified
/// </para>
/// </summary>
/// <param name="mean">The mean value for the range</param>
/// <param name="tolerance">The tolerance range</param>
public DoubleRange(double mean, Tolerance tolerance)
{
SetTolerance(mean, tolerance);
}
public void MatchIsofroms(FragmentTypes type, Tolerance tolerance, double cutoffThreshold, bool phopshoNeutralLoss, params int[] chargeStates)
{
foreach (PeptideIsoform isoform in PeptideIsoforms)
{
isoform.MatchSpectrum(type, tolerance, cutoffThreshold,phopshoNeutralLoss, chargeStates);
}
}