Property | Type | Description | |
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CoverageWeighting | double | ||
IsDbsnpVcf | bool | ||
TempFolder | string |
Property | Type | Description | |
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MeanCoverage | float | ||
MedianHetSnpsDistance | int | ||
MinimumVariantFrequenciesForInformativeSegment | int |
Method | Description | |
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AggregateCounts ( List |
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AggregateVariantCoverage ( List |
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CallVariants ( string variantFrequencyFile, string inFile, string outFile, string ploidyBedPath, string referenceFolder, string sampleName, string truthDataPath ) : int | ||
InitializePloidies ( ) : void |
Setup: Model various copy ploidies.
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Method | Description | |
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GetKnownCNForSegment ( |
Check whether we know the CN for this segment. Look for a known-CN interval that covers (at least half of) this segment. Return -1 if we don't know its CN.
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GetProjectedMeanCoverage ( double diploidCoverage ) : double[] |
Compute the expected bin counts for each copy number, given a specified bin count for CN=2 regions
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InitializeModelPoints ( |
Method | Description | |
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AssignPloidyCallsDistance ( |
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AssignPloidyCallsGaussianMixture ( ) : void |
Assign a SegmentPloidy to each CanvasSegment, based on which model matches this segment best:
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FitGaussians ( |
Fit a Gaussian mixture model. Fix the means to the model MAF and Coverage and run the EM algorithm until convergence. Compute the empirical MAF and Coverage. Fix the means to the empirical MAF and Coverage and run the EM algorithm again until convergence. Always estimate the full covariance matrix?
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GenerateReportVersusKnownCN ( ) : void |
Generate a table listing segments (and several features), and noting which are accurate (copy number exactly matches truth set) or directionally accurate (copy number and truth set are both <2, both =2, or both >2) This table will become our collection of feature vectors for training q-scores!
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public static AggregateCounts ( List |
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segments | List |
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return | float[] |
public static AggregateVariantCoverage ( List |
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segments | List |
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return | int |
public CallVariants ( string variantFrequencyFile, string inFile, string outFile, string ploidyBedPath, string referenceFolder, string sampleName, string truthDataPath ) : int | ||
variantFrequencyFile | string | |
inFile | string | |
outFile | string | |
ploidyBedPath | string | |
referenceFolder | string | |
sampleName | string | |
truthDataPath | string | |
return | int |
protected GetKnownCNForSegment ( |
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segment | ||
return | int |
protected static GetProjectedMeanCoverage ( double diploidCoverage ) : double[] | ||
diploidCoverage | double | |
return | double[] |
protected InitializeModelPoints ( |
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model | ||
return | List |
protected static int MinimumVariantFrequenciesForInformativeSegment | ||
return | int |