C# Class CanvasCommon.CopyNumberOracle

This class represents a set of known copy number calls ("truth set"), useful for training models.

Exibir arquivo Open project: Illumina/canvas Class Usage Examples

Public Properties

Property	Type	Description
KnownCN	List>.Dictionary

Public Methods

Method	Description
GetKnownCNForSegment ( CanvasSegment segment ) : int
GetKnownClonalityForSegment ( CanvasSegment segment ) : double
LoadKnownCN ( string oraclePath ) : void

Protected Methods

Method	Description
LoadKnownCNBed ( string oracleBedPath ) : void	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.
LoadKnownCNVCF ( string oracleVCFPath ) : void

Method Details

GetKnownCNForSegment() public method

public GetKnownCNForSegment ( CanvasSegment segment ) : int
segment	CanvasSegment
return	int

GetKnownClonalityForSegment() public method

public GetKnownClonalityForSegment ( CanvasSegment segment ) : double
segment	CanvasSegment
return	double

LoadKnownCN() public method

public LoadKnownCN ( string oraclePath ) : void
oraclePath	string
return	void

LoadKnownCNBed() 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 LoadKnownCNBed ( string oracleBedPath ) : void
oracleBedPath	string
return	void

LoadKnownCNVCF() protected method

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

Property Details

KnownCN public_oe property

public Dictionary> KnownCN
return	List>.Dictionary