C# Класс CanvasClean.CanvasClean

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Открытые методы

Метод	Описание
GetLocalStandardDeviationAverage ( List list, List chromosome ) : double	Calculates Standard Deviation separately for each chromosome and output their average

Приватные методы

Метод	Описание
DebugPrintCountsByGC ( List bins, string filePath ) : void	Debugging option - save off a table of counts by GC bin.
GetWeightedCounts ( List countsByGC, int gcBin ) : float>>.List	In case there are not enough read counts for a GC bin, construct a weighted list of read counts. Values from target bin i get full weight, the two neighboring bins get half weight, two-away neighbors get 1/4 weight, etc.
Main ( string args ) : int
NormalizeByGC ( List bins, NexteraManifest manifest = null ) : void	Perform a simple GC normalization.
NormalizeByGC ( List bins, NexteraManifest manifest, CanvasGCNormalizationMode mode ) : void	Perform GC normalization depending on the mode
NormalizeVarianceByGC ( List bins, NexteraManifest manifest = null ) : bool	Perform variance stabilization by GC bins.
RemoveBigBins ( List bins ) : List	Removes bins that are genomically large. Typically centromeres and other nasty regions.
RemoveBinsWithExtremeGC ( List bins, int threshold, NexteraManifest manifest = null ) : List	Remove bins with extreme GC content.
RemoveBinsWithExtremeLocalSD ( List bins, double localSDaverage, double threshold, string outFile ) : List	Remove bin regions with extreme local standard deviation (SD). Assume that MadOfDiffs has been set in GetLocalStandardDeviationAverage().
RemoveOutliers ( List bins ) : List	Removes point outliers from the dataset.
ShowHelp ( OptionSet p ) : void	Displays help at the command line.
SignificantlyDifferent ( float a, float b ) : bool	Determine if two Poisson counts are unlikely to have come from the same distribution.
getLocalStandardDeviation ( List bins ) : double	Estimate local standard deviation (SD).

Описание методов

GetLocalStandardDeviationAverage() публичный статический Метод

Calculates Standard Deviation separately for each chromosome and output their average

public static GetLocalStandardDeviationAverage ( List list, List chromosome ) : double
list	List
chromosome	List
Результат	double