Package Accuracy
Class AccuracyCalculator
- java.lang.Object
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- Accuracy.AccuracyCalculator
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public class AccuracyCalculator extends java.lang.Object
Calculates accuracy statistics
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
AccuracyCalculator.AccuracyMethod
Represents the accuracy method to be used for optimization
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static double
accuracy(java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeCall> compareTo)
Calculates the percentage of genotypes called correctlystatic AccuracyStats
accuracyStats(java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeCall> compareTo, java.util.List<SingleGenotypeMasked> depths)
Calculates various statistics concerning the genotypes called correctlystatic double
correlation(java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeCall> compareTo, java.util.List<SingleGenotypeMasked> masked)
Calculates the correlation between correct and imputed genotypes
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Method Detail
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accuracy
public static double accuracy(java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeCall> compareTo)
Calculates the percentage of genotypes called correctly- Parameters:
correct
- The correct genotypescompareTo
- The genotypes to test- Returns:
- Percentage accuracy
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correlation
public static double correlation(java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeCall> compareTo, java.util.List<SingleGenotypeMasked> masked)
Calculates the correlation between correct and imputed genotypes- Parameters:
correct
- The correct genotypescompareTo
- The genotypes to testmasked
- List of masked genotypes (contains the MAF of each genotype)- Returns:
- Percentage accuracy
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accuracyStats
public static AccuracyStats accuracyStats(java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeCall> compareTo, java.util.List<SingleGenotypeMasked> depths)
Calculates various statistics concerning the genotypes called correctly- Parameters:
correct
- The correct genotypescompareTo
- the genotypes to testdepths
- The depth (i.e. number of reads) used for each genotype- Returns:
- Accuracy statistics
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