C# Class Coon.Compass.FdrOptimizer.FdrOptimizer

Show file Open project: dbaileychess/Compass Class Usage Examples

Public Methods

Method	Description
FdrOptimizer ( IList csvFilepaths, string rawFolder, IList fixedModifications, double maximumFalseDiscoveryRate, double maximumPPMError, UniquePeptideType uniquePeptideType, string outputFolder, bool isBatched = false, bool is2DFDR = true, bool includeFixedMods = false, double evalueThresholdForPPMError = 1e-2 ) : System
Optimize ( ) : void

Protected Methods

Method	Description
OnFinished ( EventArgs e ) : void
OnStarting ( EventArgs e ) : void
OnUpdateLog ( StatusEventArgs e ) : void
OnUpdateProgress ( ProgressEventArgs e ) : void

Private Methods

Method	Description
Calculate2DFdr ( IList csvFiles, bool isBatched = false, int steps = 250, double minimumIncrement = 0.05 ) : void
CalculateBasicFDR ( IList csvFiles, bool isBatched = false ) : void
CalculateBestPPMError ( IEnumerable inputPeptides, double maximumFalseDisoveryRate = 0.01, int steps = 10, double minimumIncrement = 0.05 ) : double>.Tuple
Cleanup ( ) : void
Log ( string message ) : void
ReadInCSVFiles ( IEnumerable csvFilePaths, IList fixedModifications, int numberOfTopHits = 1 ) : IEnumerable
ReducePsms ( IList csvFiles, UniquePeptideType uniquePeptideType, bool isBatched = false ) : void
Setup ( ) : void
UpdatePsmInformation ( IList csvFiles, string rawFolder, bool useMedian = true ) : void
WriteFiles ( IEnumerable csvFiles, bool isBatched = false ) : void

Method Details

FdrOptimizer() public method

public FdrOptimizer ( IList csvFilepaths, string rawFolder, IList fixedModifications, double maximumFalseDiscoveryRate, double maximumPPMError, UniquePeptideType uniquePeptideType, string outputFolder, bool isBatched = false, bool is2DFDR = true, bool includeFixedMods = false, double evalueThresholdForPPMError = 1e-2 ) : System
csvFilepaths	IList
rawFolder	string
fixedModifications	IList
maximumFalseDiscoveryRate	double
maximumPPMError	double
uniquePeptideType	UniquePeptideType
outputFolder	string
isBatched	bool
is2DFDR	bool
includeFixedMods	bool
evalueThresholdForPPMError	double
return	System

OnFinished() protected method

protected OnFinished ( EventArgs e ) : void
e	System.EventArgs
return	void

OnStarting() protected method

protected OnStarting ( EventArgs e ) : void
e	System.EventArgs
return	void

OnUpdateLog() protected method

protected OnUpdateLog ( StatusEventArgs e ) : void
e	StatusEventArgs
return	void

OnUpdateProgress() protected method

protected OnUpdateProgress ( ProgressEventArgs e ) : void
e	ProgressEventArgs
return	void

Optimize() public method

public Optimize ( ) : void
return	void