C# 클래스 CanvasCommon.CanvasSegment

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

공개 프로퍼티들

프로퍼티	타입	설명
Counts	List
Filter	string
MajorChromosomeCount	int?
ModelDistance	double
QScore	double
RunnerUpModelDistance	double
VariantFrequencies	List
VariantTotalCoverage	List
cnSwaped	string

공개 메소드들

메소드	설명
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.

비공개 메소드들

메소드	설명
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.

메소드 상세

AssignQualityScores() 공개 정적인 메소드

Apply quality scores.

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

CanvasSegment() 공개 메소드

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

ComputeQScore() 공개 메소드

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

ExpectedCount() 공개 정적인 메소드

Compute the median count from a list of segments.

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

GetCnvType() 공개 메소드

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

GetQScorePredictor() 공개 메소드

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

GetSegmentsByChromosome() 공개 정적인 메소드

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

MergeIn() 공개 메소드

Merge another neighboring segment into this one.

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

MergeSegments() 공개 정적인 메소드

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
리턴	void

MergeSegmentsUsingExcludedIntervals() 공개 정적인 메소드

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

ReadSegments() 공개 정적인 메소드

Loads in data produced by CanvasPartition.exe.

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

WriteCoveragePlotData() 공개 정적인 메소드

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
리턴	void

WriteSegments() 공개 정적인 메소드

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
리턴	void

프로퍼티 상세

Counts 공개적으로 프로퍼티

public List Counts
리턴	List

Filter 공개적으로 프로퍼티

public string Filter
리턴	string

MajorChromosomeCount 공개적으로 프로퍼티

public int? MajorChromosomeCount
리턴	int?

ModelDistance 공개적으로 프로퍼티

public double ModelDistance
리턴	double

QScore 공개적으로 프로퍼티

public double QScore
리턴	double

RunnerUpModelDistance 공개적으로 프로퍼티

public double RunnerUpModelDistance
리턴	double

VariantFrequencies 공개적으로 프로퍼티

public List VariantFrequencies
리턴	List

VariantTotalCoverage 공개적으로 프로퍼티

public List VariantTotalCoverage
리턴	List

cnSwaped 공개적으로 프로퍼티

public string cnSwaped
리턴	string