public ExperimentalProteoform(string accession, IAggregatable root, bool is_target)
: base(accession)
{
quant = new QuantitativeProteoformValues(this);
this.root = root;
this.is_target = is_target;
}
public void computeIndividualExperimentalProteoformFDRs(List <ExperimentalProteoform> satisfactoryProteoforms, List <TusherStatistic> permutedTestStatistics, List <TusherStatistic> sortedProteoformTestStatistics)
{
Parallel.ForEach(satisfactoryProteoforms, eP =>
{
eP.quant.TusherValues2.roughSignificanceFDR = QuantitativeProteoformValues.computeExperimentalProteoformFDR(eP.quant.TusherValues2.relative_difference, permutedTestStatistics, satisfactoryProteoforms.Count, sortedProteoformTestStatistics);
});
}
public List <BiorepIntensity> make_biorepIntensityList <T>(List <T> lt_quant_components, List <T> hv_quant_components, IEnumerable <string> ltConditionStrings, IEnumerable <string> hvConditionStrings)
where T : IBiorepable
{
quant = new QuantitativeProteoformValues(this); //Reset quantitation if starting over from biorep requirements
List <BiorepIntensity> biorepIntensityList = new List <BiorepIntensity>();
foreach (string condition in ltConditionStrings.ToList())
{
foreach (int b in lt_quant_components.Where(c => c.input_file.lt_condition == condition).Select(c => c.input_file.biological_replicate).Distinct())
{
biorepIntensityList.Add(new BiorepIntensity(true, false, b, condition, lt_quant_components.Where(c => c.input_file.biological_replicate == b).Sum(i => i.intensity_sum)));
}
}
if (SaveState.lollipop.neucode_labeled)
{
foreach (string condition in hvConditionStrings.ToList())
{
foreach (int b in hv_quant_components.Where(c => c.input_file.hv_condition == condition).Select(c => c.input_file.biological_replicate).Distinct())
{
biorepIntensityList.Add(new BiorepIntensity(false, false, b, condition, hv_quant_components.Where(c => c.input_file.biological_replicate == b).Sum(i => i.intensity_sum)));
}
}
}
this.biorepIntensityList = biorepIntensityList;
return(biorepIntensityList);
}
public ExperimentalProteoform(string accession, IAggregatable root, List <IAggregatable> candidate_observations, bool is_target)
: base(accession)
{
quant = new QuantitativeProteoformValues(this);
this.root = root;
this.aggregated.AddRange(candidate_observations.Where(p => this.includes(p, this.root)));
this.calculate_properties();
this.root = this.aggregated.OrderByDescending(a => a.intensity_sum).FirstOrDefault();
}
/// <summary>
/// Returns imputed intensities for a certain condition for biological replicates this proteoform was not observed in.
/// </summary>
/// <param name="observedBftIntensities"></param>
/// <param name="bkgdAverageIntensity"></param>
/// <param name="bkgdStDev"></param>
/// <param name="condition"></param>
/// <param name="bioreps"></param>
/// <returns></returns>
public static List <BiorepIntensity> imputedIntensities(IEnumerable <BiorepIntensity> observedBioreps, decimal bkgdAverageIntensity, decimal bkgdStDev, string condition, List <string> bioreps, bool useRandomSeed, Random seeded)
{
//bkgdAverageIntensity is log base 2
//bkgdStDev is log base 2
return((
from biorep in bioreps
where !observedBioreps.Any(k => k.condition == condition && k.biorep == biorep)
select new BiorepIntensity(true, biorep, condition, QuantitativeProteoformValues.imputed_intensity(bkgdAverageIntensity, bkgdStDev, useRandomSeed, seeded)))
.ToList());
}
public List <BiorepIntensity> make_biorepIntensityList <T>(List <T> lt_quant_components, List <T> hv_quant_components, IEnumerable <string> ltConditionStrings, IEnumerable <string> hvConditionStrings)
where T : IFileIntensity
{
quant = new QuantitativeProteoformValues(this); //Reset quantitation if starting over from biorep requirements
List <BiorepIntensity> biorepIntensityList = new List <BiorepIntensity>();
List <BiorepTechrepIntensity> biotechIntensityList = new List <BiorepTechrepIntensity>();
foreach (string condition in ltConditionStrings.Concat(hvConditionStrings).Distinct().ToList())
{
List <T> quants_from_condition = lt_quant_components.Where(c => c.input_file.lt_condition == condition).Concat(hv_quant_components.Where(c => c.input_file.hv_condition == condition)).ToList();
List <InputFile> files = quants_from_condition.Select(x => x.input_file).ToList();
List <string> bioreps = quants_from_condition.Select(c => c.input_file.biological_replicate).Distinct().ToList();
biorepIntensityList.AddRange(bioreps.Select(b => new BiorepIntensity(false, b, condition, quants_from_condition.Where(c => c.input_file.biological_replicate == b).Sum(i => i.intensity_sum))));
List <Tuple <string, string> > biotechs = quants_from_condition.Select(c => new Tuple <string, string>(c.input_file.biological_replicate, c.input_file.technical_replicate)).Distinct().ToList();
biotechIntensityList.AddRange(biotechs.Select(x => new BiorepTechrepIntensity(false, x.Item1, condition, x.Item2, quants_from_condition.Where(c => c.input_file.biological_replicate == x.Item1 && c.input_file.technical_replicate == x.Item2).Sum(asdf => asdf.intensity_sum))));
}
this.biorepIntensityList = biorepIntensityList;
this.biorepTechrepIntensityList = biotechIntensityList;
return(biorepIntensityList);
}
// COPYING CONSTRUCTOR
public ExperimentalProteoform(ExperimentalProteoform eP)
: base(eP.accession, eP.modified_mass, eP.lysine_count, eP.is_target)
{
copy_aggregate(eP);
quant = new QuantitativeProteoformValues(this);
}
/// <summary>
/// Returns imputed intensities for a certain condition for biological replicates this proteoform was not observed in.
/// </summary>
/// <param name="observedBioreps"></param>
/// <param name="bkgdAverageIntensity"></param>
/// <param name="bkgdStDev"></param>
/// <param name="condition"></param>
/// <param name="bioreps"></param>
/// <returns></returns>
public static List <BiorepTechrepIntensity> imputedIntensities(List <BiorepTechrepIntensity> observedBioreps, IEnumerable <InputFile> files, decimal bkgdAverageIntensity, decimal bkgdStDev, string condition, List <string> bioreps, bool useRandomSeed, Random seeded)
{
//bkgdAverageIntensity is log base 2
//bkgdStDev is log base 2
List <Tuple <string, string> > bt = files.Select(x => new Tuple <string, string>(x.biological_replicate, x.technical_replicate)).Distinct().ToList();
return((
from x in bt
where !observedBioreps.Any(k => k.condition == condition && k.biorep == x.Item1 && k.techrep == x.Item2)
select new BiorepTechrepIntensity(true, x.Item1, condition, x.Item2, QuantitativeProteoformValues.imputed_intensity(bkgdAverageIntensity, bkgdStDev, useRandomSeed, seeded)))
.ToList());
}