C# Class EvaluateCNV.CNVChecker

Datei anzeigen Open project: Illumina/canvas Class Usage Examples

Public Methods

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

Protected Methods

Method	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 method

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

CountExcludedBasesInTruthSetIntervals() protected method

protected CountExcludedBasesInTruthSetIntervals ( ) : void
return	void

Evaluate() public method

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
return	void

GetCnvCallsFromBed() protected method

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

GetCnvCallsFromVcf() protected method

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

GetCopyNumber() protected method

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

LoadIntervalsFromBed() protected method

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
return	List>.Dictionary

LoadKnownCN() protected method

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

LoadKnownCNVCF() protected method

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

LoadRegionsOfInterest() protected method

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

SummarizeTruthSetStatistics() protected method

protected SummarizeTruthSetStatistics ( ) : void
return	void