Package org.snpeff.geneSets.algorithm

Class EnrichmentAlgorithm

java.lang.Object
org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
Direct Known Subclasses:
EnrichmentAlgorithmGreedy, FisherPValueAlgorithm, NoneAlgorithm, RankSumPValueAlgorithm
public abstract class EnrichmentAlgorithm extends Object
A generic enrichment algorithm for selecting gene-sets from a collection of gene-sets
Author:
pcingola

  • Field Details

    • HTML_TD_GENES_MAX_LEN

      public static final int HTML_TD_GENES_MAX_LEN
      See Also:

    • HTML_BG_COLOR

      public static final String[] HTML_BG_COLOR

    • HTML_BG_COLOR_TITLE

      public static final String HTML_BG_COLOR_TITLE
      See Also:

  • Constructor Details

    • EnrichmentAlgorithm

      public EnrichmentAlgorithm(GeneSets geneSets, int numberToSelect)

  • Method Details

    • getMaxPvalueAdjusted

      public double getMaxPvalueAdjusted()

    • getOutput

      public StringBuilder getOutput()

    • isShow

      protected boolean isShow(Result result)
      Showld we show this result or should the output be filtered?
      Parameters:
      result -
      Returns:

    • print

      protected void print(String str)

    • select

      public Result select()
      Select the 'best' gene sets
      Returns:

    • setDebug

      public void setDebug(boolean debug)

    • setFilterOutputGeneSets

      public void setFilterOutputGeneSets(Set<String> filterOutputGeneSets)

    • setHtmlTable

      public void setHtmlTable(boolean htmlTable)

    • setMaxGeneSetSize

      public void setMaxGeneSetSize(int maxGeneSetSize)

    • setMaxPValue

      public void setMaxPValue(double maxPValue)

    • setMaxPvalueAdjusted

      public void setMaxPvalueAdjusted(double maxPvalueAdjusted)

    • setMinGeneSetSize

      public void setMinGeneSetSize(int minGeneSetSize)

    • setVerbose

      public void setVerbose(boolean verbose)