Package Accuracy

Class AccuracyCalculator


  • public class AccuracyCalculator
    extends java.lang.Object
    Calculates accuracy statistics
    • Method Detail

      • 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 genotypes
        compareTo - The genotypes to test
        Returns:
        Percentage accuracy
      • 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 genotypes
        compareTo - The genotypes to test
        masked - List of masked genotypes (contains the MAF of each genotype)
        Returns:
        Percentage accuracy
      • 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 genotypes
        compareTo - the genotypes to test
        depths - The depth (i.e. number of reads) used for each genotype
        Returns:
        Accuracy statistics