C# Class EvaluateCNV.CNVChecker

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Méthodes publiques

Méthode	Description
Evaluate ( string truthSetPath, string cnvCallsPath, string excludedBed, string outputPath, string ROIBedPath, double heterogeneityFraction ) : void

Méthodes protégées

Méthode	Description
ComputeAccuracy ( string truthSetPath, string cnvCallsPath, StreamWriter outputWriter, bool includePassingOnly ) : void
CountExcludedBasesInTruthSetIntervals ( ) : void
GetCnvCallsFromBed ( string bedPath, int cnIndices = null ) : IEnumerable
GetCnvCallsFromVcf ( string vcfPath, bool includePassingOnly ) : IEnumerable
GetCopyNumber ( VcfVariant variant, int &end ) : int
LoadIntervalsFromBed ( string oracleBedPath, bool getCN, double heterogeneityFraction ) : List>.Dictionary	Load known CN data from a .bed file. File lines have fields: chromosome, start, end, chromcountA, chromcountB So, copy number is the sum of the last 2 fields, major chromosome count is the max of the last 2 fields.
LoadKnownCN ( string oraclePath, double heterogeneityFraction ) : void
LoadKnownCNVCF ( string oracleVCFPath ) : void
LoadRegionsOfInterest ( string bedPath ) : void
SummarizeTruthSetStatistics ( ) : void

Method Details

ComputeAccuracy() protected méthode

protected ComputeAccuracy ( string truthSetPath, string cnvCallsPath, StreamWriter outputWriter, bool includePassingOnly ) : void
truthSetPath	string
cnvCallsPath	string
outputWriter	System.IO.StreamWriter
includePassingOnly	bool
Résultat	void

CountExcludedBasesInTruthSetIntervals() protected méthode

protected CountExcludedBasesInTruthSetIntervals ( ) : void
Résultat	void

Evaluate() public méthode

public Evaluate ( string truthSetPath, string cnvCallsPath, string excludedBed, string outputPath, string ROIBedPath, double heterogeneityFraction ) : void
truthSetPath	string
cnvCallsPath	string
excludedBed	string
outputPath	string
ROIBedPath	string
heterogeneityFraction	double
Résultat	void

GetCnvCallsFromBed() protected méthode

protected GetCnvCallsFromBed ( string bedPath, int cnIndices = null ) : IEnumerable
bedPath	string
cnIndices	int
Résultat	IEnumerable

GetCnvCallsFromVcf() protected méthode

protected GetCnvCallsFromVcf ( string vcfPath, bool includePassingOnly ) : IEnumerable
vcfPath	string
includePassingOnly	bool
Résultat	IEnumerable

GetCopyNumber() protected méthode

protected GetCopyNumber ( VcfVariant variant, int &end ) : int
variant	VcfVariant
end	int
Résultat	int

LoadIntervalsFromBed() protected méthode

Load known CN data from a .bed file. File lines have fields: chromosome, start, end, chromcountA, chromcountB So, copy number is the sum of the last 2 fields, major chromosome count is the max of the last 2 fields.

protected LoadIntervalsFromBed ( string oracleBedPath, bool getCN, double heterogeneityFraction ) : List>.Dictionary
oracleBedPath	string
getCN	bool
heterogeneityFraction	double
Résultat	List>.Dictionary

LoadKnownCN() protected méthode

protected LoadKnownCN ( string oraclePath, double heterogeneityFraction ) : void
oraclePath	string
heterogeneityFraction	double
Résultat	void

LoadKnownCNVCF() protected méthode

protected LoadKnownCNVCF ( string oracleVCFPath ) : void
oracleVCFPath	string
Résultat	void

LoadRegionsOfInterest() protected méthode

protected LoadRegionsOfInterest ( string bedPath ) : void
bedPath	string
Résultat	void

SummarizeTruthSetStatistics() protected méthode

protected SummarizeTruthSetStatistics ( ) : void
Résultat	void