Package org.snpeff.stats

Class ObservedOverExpected

    • Method Summary

      All Methods Instance Methods Abstract Methods Concrete Methods 
      Modifier and Type Method Description
      abstract double expected​(java.lang.String sequence)  
      double expected​(Exon e)
      Expected number of sequences (average between plus and minus strand)
      double expected​(Gene g)
      Expected number of sequences (average between plus and minus strand)
      double expected​(Transcript t)
      Expected number of sequences (average between plus and minus strand)
      abstract int observed​(java.lang.String sequence)  
      int observed​(Exon e)
      Observed sequence (average between plus and minus strand)
      int observed​(Gene g)
      Observed sequence (average between plus and minus strand)
      int observed​(Transcript t)
      Observed sequence (average between plus and minus strand)
      int observedChg​(java.lang.String sequence)
      Count the number of CHG in this sequence
      double oe​(java.lang.String sequence)
      Observed over expected ratio
      double oe​(Exon e)
      Observed over expected ratio
      double oe​(Gene g)
      Observed over expected ratio
      double oe​(Transcript t)
      Observed over expected ratio

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • ObservedOverExpected

        public ObservedOverExpected()

    • Method Detail

      • expected

        public double expected​(Exon e)
        Expected number of sequences (average between plus and minus strand)
        Parameters:
        e - : Exon
        Returns:

      • expected

        public double expected​(Gene g)
        Expected number of sequences (average between plus and minus strand)
        Parameters:
        t - : Transcript
        Returns:

      • expected

        public abstract double expected​(java.lang.String sequence)

      • expected

        public double expected​(Transcript t)
        Expected number of sequences (average between plus and minus strand)
        Parameters:
        t - : Transcript
        Returns:

      • observed

        public int observed​(Exon e)
        Observed sequence (average between plus and minus strand)
        Parameters:
        e - : Exon
        Returns:

      • observed

        public int observed​(Gene g)
        Observed sequence (average between plus and minus strand)
        Parameters:
        g - : Gene
        Returns:

      • observed

        public abstract int observed​(java.lang.String sequence)

      • observed

        public int observed​(Transcript t)
        Observed sequence (average between plus and minus strand)
        Parameters:
        t - : Transcript
        Returns:

      • observedChg

        public int observedChg​(java.lang.String sequence)
        Count the number of CHG in this sequence
        Parameters:
        sequence -
        Returns:

      • oe

        public double oe​(Exon e)
        Observed over expected ratio
        Parameters:
        Exon -
        Returns:

      • oe

        public double oe​(Gene g)
        Observed over expected ratio
        Parameters:
        Gene -
        Returns:

      • oe

        public double oe​(java.lang.String sequence)
        Observed over expected ratio
        Parameters:
        sequence -
        Returns:

      • oe

        public double oe​(Transcript t)
        Observed over expected ratio
        Parameters:
        Transcript -
        Returns: