public class AccuracyCalculator
extends java.lang.Object
Modifier and Type | Class | Description |
---|---|---|
static class |
AccuracyCalculator.AccuracyMethod |
Represents the accuracy method to be used for optimization
|
Modifier and Type | Method | Description |
---|---|---|
static double |
accuracy(java.util.List<SingleGenotypeCall> correct,
java.util.List<SingleGenotypeCall> compareTo) |
Calculates the percentage of genotypes called correctly
|
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
|
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
|
public static double accuracy(java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeCall> compareTo)
correct
- The correct genotypescompareTo
- The genotypes to testpublic static double correlation(java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeCall> compareTo, java.util.List<SingleGenotypeMasked> masked)
correct
- The correct genotypescompareTo
- The genotypes to testmasked
- List of masked genotypes (contains the MAF of each genotype)public static AccuracyStats accuracyStats(java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeCall> compareTo, java.util.List<SingleGenotypeMasked> depths)
correct
- The correct genotypescompareTo
- the genotypes to testdepths
- The depth (i.e. number of reads) used for each genotype