C# 클래스 EvaluateCNV.CNVChecker

파일 보기 프로젝트 열기: Illumina/canvas 1 사용 예제들

공개 메소드들

메소드	설명
Evaluate ( string truthSetPath, string cnvCallsPath, string excludedBed, string outputPath, string ROIBedPath, double heterogeneityFraction ) : void

보호된 메소드들

메소드	설명
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

메소드 상세

ComputeAccuracy() 보호된 메소드

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

CountExcludedBasesInTruthSetIntervals() 보호된 메소드

protected CountExcludedBasesInTruthSetIntervals ( ) : void
리턴	void

Evaluate() 공개 메소드

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
리턴	void

GetCnvCallsFromBed() 보호된 메소드

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

GetCnvCallsFromVcf() 보호된 메소드

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

GetCopyNumber() 보호된 메소드

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

LoadIntervalsFromBed() 보호된 메소드

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
리턴	List>.Dictionary

LoadKnownCN() 보호된 메소드

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

LoadKnownCNVCF() 보호된 메소드

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

LoadRegionsOfInterest() 보호된 메소드

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

SummarizeTruthSetStatistics() 보호된 메소드

protected SummarizeTruthSetStatistics ( ) : void
리턴	void