C# Class CanvasPartition.Segmentation

Show file Open project: Illumina/canvas Class Usage Examples

Public Properties

Property	Type	Description
Alpha	double
DefaultAlpha	double
UndoMethod	SegmentSplitUndo

Public Methods

Method	Description
SegmentGenome ( string outPath, SegmentationMethod method, bool isGermline ) : void
Segmentation ( string inputBinPath, string forbiddenBedPath, string dataType = "logratio", int maxInterBinDistInSegment = 1000000 ) : System

Private Methods

Method	Description
CBS ( uint nPerm = 10000, string pMethod = "hybrid", int minWidth = 2, int kMax = 25, uint nMin = 200, double eta = 0.05, uint sbdry = null, double trim = 0.025, double undoPrune = 0.05, double undoSD = 3, int verbose = 1 ) : void	CBS: circular binary segmentation porting the R function segment in DNAcopy
GetDummySegmentationResults ( ) : GenomeSegmentationResults
ReadBEDInput ( ) : void	Assume that the rows are sorted by the start position and ascending order
Wavelets ( bool isGermline, double thresholdLower = 5, double thresholdUpper = 80, int minSize = 10, int verbose = 1 ) : void	Wavelets: unbalanced HAAR wavelets segmentation
WriteCanvasPartitionResults ( string outPath ) : void

Method Details

SegmentGenome() public method

public SegmentGenome ( string outPath, SegmentationMethod method, bool isGermline ) : void
outPath	string
method	SegmentationMethod
isGermline	bool
return	void

Segmentation() public method

public Segmentation ( string inputBinPath, string forbiddenBedPath, string dataType = "logratio", int maxInterBinDistInSegment = 1000000 ) : System
inputBinPath	string
forbiddenBedPath	string
dataType	string
maxInterBinDistInSegment	int
return	System

Property Details

Alpha public property

public double Alpha
return	double

DefaultAlpha public static property

public static double DefaultAlpha
return	double

UndoMethod public property

public SegmentSplitUndo UndoMethod
return	SegmentSplitUndo