public void Calculate(IIdentifiedResult proteins, Dictionary <string, List <string> > datasets)
{
if (proteins == null || proteins.Count == 0)
{
throw new ArgumentNullException("Argument proteins cannot be null or empty in NSAFProteinLabelfreeQuantificationCalculator.Calculate");
}
if (proteins.Count > 0 && proteins.Any(m => m[0].Sequence == null))
{
throw new Exception("NSAF Quantification Calculator needs protein sequence information.");
}
foreach (var g in proteins)
{
var lr = new LabelfreeResult();
foreach (var key in datasets.Keys)
{
lr[key] = new LabelfreeValue();
}
foreach (var p in g)
{
p.SetLabelfreeResult(lr);
}
}
double zeroCount = 0.16;
foreach (var key in datasets.Keys)
{
List <string> exps = datasets[key];
double allnsaf = 0.0;
foreach (var g in proteins)
{
var lr = g[0].GetLabelfreeResult();
var lv = lr[key];
lv.Count = g.GetPeptides().Count(m => exps.Contains(m.Query.FileScan.Experimental));
var sc = (double)(lv.Count);
lv.Value = sc / g[0].Sequence.Length;
allnsaf += lv.Value;
}
foreach (var g in proteins)
{
var lr = g[0].GetLabelfreeResult();
var lv = lr[key];
var nsaf = lv.Value;
if (nsaf == 0)
{
nsaf = zeroCount / g[0].Sequence.Length;
}
lv.Value = Math.Log(nsaf / allnsaf);
}
}
}
public static void SetLabelfreeResult(this IAnnotation ann, LabelfreeResult item)
{
ann.Annotations[KEY] = item;
}
public void Calculate(IIdentifiedResult proteins, Dictionary <string, List <string> > datasets)
{
if (proteins == null || proteins.Count == 0)
{
throw new ArgumentNullException("Argument proteins cannot be null or empty in SInProteinLabelfreeQuantificationCalculator.Calculate");
}
if (proteins.Count > 0 && proteins.Any(m => m[0].Sequence == null))
{
throw new Exception("SIn Quantification Calculator needs protein sequence information.");
}
var spectra = proteins.GetSpectra();
if (spectra.Any(m => m.MatchedTIC == 0))
{
throw new Exception("SIn Quantification Calculator needs matched ion count information.");
}
//build experimental/dataset map
var expDatasetMap = new Dictionary <string, string>();
foreach (var ds in datasets)
{
ds.Value.ForEach(m => expDatasetMap[m] = ds.Key);
}
var minTic = spectra.Min(m => m.MatchedTIC) / 6;
//group spectra by dataset
var spectraDatasetGroup = spectra.GroupBy(m => expDatasetMap[m.Query.FileScan.Experimental]);
//build dataset/sum(tic) map
var datasetSumOfTicMap = new Dictionary <string, double>();
foreach (var entry in spectraDatasetGroup)
{
datasetSumOfTicMap[entry.Key] = entry.Sum(m => m.MatchedTIC);
}
//calculate SIn of each protein
foreach (var g in proteins)
{
var lr = new LabelfreeResult();
foreach (var key in datasets.Keys)
{
lr[key] = new LabelfreeValue();
}
foreach (var p in g)
{
p.SetLabelfreeResult(lr);
}
}
foreach (var dataset in datasets.Keys)
{
List <string> exps = datasets[dataset];
double sumOfTic = datasetSumOfTicMap[dataset];
foreach (var g in proteins)
{
var lr = g[0].GetLabelfreeResult();
var lv = lr[dataset];
//get spectra in current dataset
var specs = (from p in g.GetPeptides()
where exps.Contains(p.Query.FileScan.Experimental)
select p).ToList();
if (specs.Count > 0)
{
lv.Count = specs.Count();
//get SI of the protein in current dataset
lv.Value = specs.Sum(m => m.MatchedTIC);
}
else
{
lv.Count = 0;
//set as minimum TIC value.
lv.Value = minTic;
}
//SI(GI) = SI / sumOfTic
//SI(N) = SI(GI) / Length(Protein)
lv.Value = Math.Log10(lv.Value / sumOfTic / g[0].Sequence.Length);
}
}
}