C# Class Coon.Compass.Procyon.QuantFile

Exibir arquivo Open project: dbaileychess/Compass Class Usage Examples

Public Methods

Method	Description
AddComparison ( Comparison comparison, ValueType typeOfValue ) : void
GroupQuantData ( ) : void
MulitpleComparisonCorrection ( string multCompString, string thresholdTypeString, double sigThreshold ) : void
NormalizeDataSet ( bool noNormalize, bool sumNormalize, bool medianNormalize, string uniprotHeader, string normalizationString, List uniprotListForNormalization ) : void
PerformSignificanceTest ( string sigTestingString, double sigThreshold, ValueType typeOfValue ) : void
QuantFile ( List quantFiles, string>.Dictionary fileNameAndHeadertoUniqueGroupName ) : System
QuantFile ( string fileLocation, List quantHeaders ) : System
TestAnnotationEnrichment ( string annotationString, List annotationsToAdd, AnnotationEntry>.Dictionary annotationEntryDict, Dictionary uniprotToAnnotationList, double annotationSigThreshold ) : void

Private Methods

Method	Description
AnnotateQuantEntries ( string annotationString, List annotationsToAdd, AnnotationEntry>.Dictionary annotationEntryDict, Dictionary uniprotToAnnotationList ) : void
ApplyNormalizationFactors ( ) : void
BenjaminiHochberg ( double>.Dictionary pvalueDict ) : double>.Dictionary
CreateAnnotationCountDict ( Dictionary annotationQuantListDict ) : Dictionary>
DoNotNormalizeDataSet ( Dictionary normalizationSubset ) : void
FisherExactTest ( int>.Dictionary background, int>.Dictionary test ) : double>.Dictionary
ListSignificantChangingQuantEntries ( List annotationsToAdd, Comparison comparison, string sigType, List quantEntries ) : List>.Dictionary
MedianNormalizeDataSet ( Dictionary normalizationSubset ) : void
SumNormalizeDataSet ( Dictionary normalizationSubset ) : void
TestForEnrichment ( int>.Dictionary backgroundDict, int>.Dictionary testDict, double annotationSigThreshold ) : Dictionary>

Method Details

AddComparison() public method

public AddComparison ( Comparison comparison, ValueType typeOfValue ) : void
comparison	Comparison
typeOfValue	System.ValueType
return	void

GroupQuantData() public method

public GroupQuantData ( ) : void
return	void

MulitpleComparisonCorrection() public method

public MulitpleComparisonCorrection ( string multCompString, string thresholdTypeString, double sigThreshold ) : void
multCompString	string
thresholdTypeString	string
sigThreshold	double
return	void

NormalizeDataSet() public method

public NormalizeDataSet ( bool noNormalize, bool sumNormalize, bool medianNormalize, string uniprotHeader, string normalizationString, List uniprotListForNormalization ) : void
noNormalize	bool
sumNormalize	bool
medianNormalize	bool
uniprotHeader	string
normalizationString	string
uniprotListForNormalization	List
return	void

PerformSignificanceTest() public method

public PerformSignificanceTest ( string sigTestingString, double sigThreshold, ValueType typeOfValue ) : void
sigTestingString	string
sigThreshold	double
typeOfValue	System.ValueType
return	void

QuantFile() public method

public QuantFile ( List quantFiles, string>.Dictionary fileNameAndHeadertoUniqueGroupName ) : System
quantFiles	List
fileNameAndHeadertoUniqueGroupName	string>.Dictionary
return	System

QuantFile() public method

public QuantFile ( string fileLocation, List quantHeaders ) : System
fileLocation	string
quantHeaders	List
return	System

TestAnnotationEnrichment() public method

public TestAnnotationEnrichment ( string annotationString, List annotationsToAdd, AnnotationEntry>.Dictionary annotationEntryDict, Dictionary uniprotToAnnotationList, double annotationSigThreshold ) : void
annotationString	string
annotationsToAdd	List
annotationEntryDict	AnnotationEntry>.Dictionary
uniprotToAnnotationList	Dictionary
annotationSigThreshold	double
return	void