Method | Description | |
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GetLocalStandardDeviationAverage ( List |
Calculates Standard Deviation separately for each chromosome and output their average
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Method | Description | |
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DebugPrintCountsByGC ( List |
Debugging option - save off a table of counts by GC bin.
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GetWeightedCounts ( 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.
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Main ( string args ) : int | ||
NormalizeByGC ( List |
Perform a simple GC normalization.
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NormalizeByGC ( List |
Perform GC normalization depending on the mode
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NormalizeVarianceByGC ( List |
Perform variance stabilization by GC bins.
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RemoveBigBins ( List |
Removes bins that are genomically large. Typically centromeres and other nasty regions.
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RemoveBinsWithExtremeGC ( List |
Remove bins with extreme GC content.
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RemoveBinsWithExtremeLocalSD ( List |
Remove bin regions with extreme local standard deviation (SD). Assume that MadOfDiffs has been set in GetLocalStandardDeviationAverage().
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RemoveOutliers ( List |
Removes point outliers from the dataset.
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ShowHelp ( OptionSet p ) : void |
Displays help at the command line.
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SignificantlyDifferent ( float a, float b ) : bool |
Determine if two Poisson counts are unlikely to have come from the same distribution.
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getLocalStandardDeviation ( List |
Estimate local standard deviation (SD).
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public static GetLocalStandardDeviationAverage ( List |
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list | List |
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chromosome | List |
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return | double |