Package org.gorpipe.gor.gava

Class GavaLogLikelihood

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected int casePenetrance
      Case penetrance (0 for no locus hetreogeneity, -1 for no constraint).
      protected int controlPenetrance
      Control penetrance (0 for complete penetrance, -1 for no constraint).
      protected boolean includeProtective
      Include protective variants in calculations.
      protected boolean noMaxAlleleCounts
      No max allele count for each case in dominant/recessive models.
      protected int numCases  
      protected int numControls  
      protected double upperFreqThreshold
      Upper threshold for the control allele frequency.

    • Method Summary

      All Methods Instance Methods Abstract Methods Concrete Methods 
      Modifier and Type Method Description
      double calcVariantLogLikelihood​(VariantCounts counts, int[] perm)
      Calculate the log-likelihood for a single variant (using the regular inheritance model).
      abstract double computeLogLikelihood​(java.util.List<org.gorpipe.gor.gava.CollapsedCounts> collapsedCounts, int[] perm, boolean debug)
      Compute the log-likelihood ratio for a feature.
      void setIncludeProtective​(boolean includeProtective)
      Set if protective variants should be included (default is false).
      void setPenetrance​(int controlPenetrance, int casePenetrance, boolean noMaxAlleleCounts)  
      void setSubjectCounts​(int numCases, int numControls)  
      void setUpperFreqThreshold​(double upperFreqThreshold)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • upperFreqThreshold

        protected double upperFreqThreshold
        Upper threshold for the control allele frequency.

      • controlPenetrance

        protected int controlPenetrance
        Control penetrance (0 for complete penetrance, -1 for no constraint).

      • casePenetrance

        protected int casePenetrance
        Case penetrance (0 for no locus hetreogeneity, -1 for no constraint).

      • noMaxAlleleCounts

        protected boolean noMaxAlleleCounts
        No max allele count for each case in dominant/recessive models.

      • includeProtective

        protected boolean includeProtective
        Include protective variants in calculations.

      • numCases

        protected int numCases

      • numControls

        protected int numControls

    • Constructor Detail

      • GavaLogLikelihood

        public GavaLogLikelihood()

    • Method Detail

      • setSubjectCounts

        public void setSubjectCounts​(int numCases,
                             int numControls)
        Parameters:
        numCases -
        numControls -

      • setPenetrance

        public void setPenetrance​(int controlPenetrance,
                          int casePenetrance,
                          boolean noMaxAlleleCounts)
        Parameters:
        controlPenetrance - maximum count among controls, -1 for no constraint
        casePenetrance - true if recessive/dominant with no locus heterogeneity
        noMaxAlleleCounts - true if no max allele count for each case in dominant/recessive models

      • setUpperFreqThreshold

        public void setUpperFreqThreshold​(double upperFreqThreshold)
        Parameters:
        upperFreqThreshold - upper threshold for the allele frequency

      • setIncludeProtective

        public void setIncludeProtective​(boolean includeProtective)
        Set if protective variants should be included (default is false).
        Parameters:
        includeProtective - true to include protective variants, false to exclude

      • computeLogLikelihood

        public abstract double computeLogLikelihood​(java.util.List<org.gorpipe.gor.gava.CollapsedCounts> collapsedCounts,
                                            int[] perm,
                                            boolean debug)
        Compute the log-likelihood ratio for a feature. The first numControls subjects in the given permutation are used as controls, and the remaining perm.length-numControls are used as cases.
        Parameters:
        collapsedCounts - the call counts for the subjects (with very rare variants collapsed)
        perm - permutation of the subjects
        debug - if true, print out debug information
        Returns:
        the log-likelihood

      • calcVariantLogLikelihood

        public double calcVariantLogLikelihood​(VariantCounts counts,
                                       int[] perm)
        Calculate the log-likelihood for a single variant (using the regular inheritance model).
        Parameters:
        counts - the call counts for the variant
        perm - permutation of the subjects
        Returns:
        the log-likelihood