C# Class CanvasCommon.CanvasSegment

Contains information about a genomic interval. Has functions for computing copy numbers and their likelihoods.

Datei anzeigen Open project: Illumina/canvas Class Usage Examples

Public Properties

Property	Type	Description
Counts	List
Filter	string
MajorChromosomeCount	int?
ModelDistance	double
QScore	double
RunnerUpModelDistance	double
VariantFrequencies	List
VariantTotalCoverage	List
cnSwaped	string

Public Methods

Method	Description
AssignQualityScores ( List segments, QScoreMethod qscoreMethod ) : void	Apply quality scores.
CanvasSegment ( string chr, int begin, int end, List counts ) : System
ComputeQScore ( QScoreMethod qscoreMethod ) : int
ExpectedCount ( List segments ) : double	Compute the median count from a list of segments.
GetCnvType ( int referenceCopyNumber ) : CnvType
GetQScorePredictor ( QScorePredictor predictorId ) : double
GetSegmentsByChromosome ( List segments ) : List>.Dictionary
MergeIn ( CanvasSegment s ) : void	Merge another neighboring segment into this one.
MergeSegments ( List &segments, int MinimumCallSize, int maximumMergeSpan = 10000 ) : void	Iterates through a list of segments and merges those which have the same copy number call. Also, for segments smaller than MinimumCallSize, assimilate them into the neighbor with the best quality score. Two consecutive segments are considered neighbors if they're on the same chromosome and the space between them is not too large.
MergeSegmentsUsingExcludedIntervals ( List &segments, int MinimumCallSize, Dictionary excludedIntervals ) : void	Iterates through a list of segments and merges those which have the same copy number call. Also, for segments smaller than MinimumCallSize, assimilate them into the neighbor with the best quality score. Two consecutive segments are considered neighbors if they're on the same chromosome and the space between them doesn't overlap with any excluded intervals.
ReadSegments ( string infile ) : List	Loads in data produced by CanvasPartition.exe.
WriteCoveragePlotData ( List segments, double normalDiploidCoverage, PloidyInfo referencePloidy, string filePath, string referenceFolder ) : void	Generate a tabular file with information about coverage and allele frequency for each chunk of the genome. This file can be used to generate a pretty plot of coverage versus MAF.
WriteSegments ( string outVcfPath, List segments, string wholeGenomeFastaDirectory, string sampleName, List extraHeaders, PloidyInfo ploidy, int qualityThreshold = 10 ) : void	Outputs the copy number calls to a text file.

Private Methods

Method	Description
IsForbiddenInterval ( string chr, int start, int end, Dictionary excludedIntervals ) : bool	Return true if we are not allowed to merge two segments separated by the interval (start, end).
SanityCheckChromosomeNames ( GenomeMetadata genome, List segments ) : void	Integrity check, to ensure that our reference FASTA file is in sync with our inputs.

Method Details

AssignQualityScores() public static method

Apply quality scores.

public static AssignQualityScores ( List segments, QScoreMethod qscoreMethod ) : void
segments	List
qscoreMethod	QScoreMethod
return	void

CanvasSegment() public method

public CanvasSegment ( string chr, int begin, int end, List counts ) : System
chr	string
begin	int
end	int
counts	List
return	System

ComputeQScore() public method

public ComputeQScore ( QScoreMethod qscoreMethod ) : int
qscoreMethod	QScoreMethod
return	int

ExpectedCount() public static method

Compute the median count from a list of segments.

public static ExpectedCount ( List segments ) : double
segments	List	List of segments.
return	double

GetCnvType() public method

public GetCnvType ( int referenceCopyNumber ) : CnvType
referenceCopyNumber	int
return	CnvType

GetQScorePredictor() public method

public GetQScorePredictor ( QScorePredictor predictorId ) : double
predictorId	QScorePredictor
return	double

GetSegmentsByChromosome() public static method

public static GetSegmentsByChromosome ( List segments ) : List>.Dictionary
segments	List
return	List>.Dictionary

MergeIn() public method

Merge another neighboring segment into this one.

public MergeIn ( CanvasSegment s ) : void
s	CanvasSegment	Segment to merge in.
return	void

MergeSegments() public static method

Iterates through a list of segments and merges those which have the same copy number call. Also, for segments smaller than MinimumCallSize, assimilate them into the neighbor with the best quality score. Two consecutive segments are considered neighbors if they're on the same chromosome and the space between them is not too large.

public static MergeSegments ( List &segments, int MinimumCallSize, int maximumMergeSpan = 10000 ) : void
segments	List
MinimumCallSize	int
maximumMergeSpan	int
return	void

MergeSegmentsUsingExcludedIntervals() public static method

public static MergeSegmentsUsingExcludedIntervals ( List &segments, int MinimumCallSize, Dictionary excludedIntervals ) : void
segments	List
MinimumCallSize	int
excludedIntervals	Dictionary
return	void

ReadSegments() public static method

Loads in data produced by CanvasPartition.exe.

public static ReadSegments ( string infile ) : List
infile	string	Input file.
return	List

WriteCoveragePlotData() public static method

Generate a tabular file with information about coverage and allele frequency for each chunk of the genome. This file can be used to generate a pretty plot of coverage versus MAF.

public static WriteCoveragePlotData ( List segments, double normalDiploidCoverage, PloidyInfo referencePloidy, string filePath, string referenceFolder ) : void
segments	List
normalDiploidCoverage	double
referencePloidy	PloidyInfo
filePath	string
referenceFolder	string
return	void

WriteSegments() public static method

Outputs the copy number calls to a text file.

public static WriteSegments ( string outVcfPath, List segments, string wholeGenomeFastaDirectory, string sampleName, List extraHeaders, PloidyInfo ploidy, int qualityThreshold = 10 ) : void
outVcfPath	string
segments	List
wholeGenomeFastaDirectory	string
sampleName	string
extraHeaders	List
ploidy	PloidyInfo
qualityThreshold	int
return	void

Property Details

Counts public_oe property

public List Counts
return	List

Filter public_oe property

public string Filter
return	string

MajorChromosomeCount public_oe property

public int? MajorChromosomeCount
return	int?

ModelDistance public_oe property

public double ModelDistance
return	double

QScore public_oe property

public double QScore
return	double

RunnerUpModelDistance public_oe property

public double RunnerUpModelDistance
return	double

VariantFrequencies public_oe property

public List VariantFrequencies
return	List

VariantTotalCoverage public_oe property

public List VariantTotalCoverage
return	List

cnSwaped public_oe property

public string cnSwaped
return	string