Package org.snpeff.stats

Class ObservedOverExpected

java.lang.Object
org.snpeff.stats.ObservedOverExpected
Direct Known Subclasses:
ObservedOverExpectedCHG, ObservedOverExpectedCHH, ObservedOverExpectedCpG
public abstract class ObservedOverExpected extends Object
Observed over expected values (o/e) ratios E.g.: CpG dinucleotides in a sequence
Author:
pcingola

  • Constructor Details

    • ObservedOverExpected

      public ObservedOverExpected()

  • Method Details

    • 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(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(String sequence)

    • observed

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

    • observedChg

      public int observedChg(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(String sequence)
      Observed over expected ratio
      Parameters:
      sequence -
      Returns:

    • oe

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