Package org.snpeff.geneSets

Class GeneSetsRanked

java.lang.Object
org.snpeff.geneSets.GeneSets
org.snpeff.geneSets.GeneSetsRanked
All Implemented Interfaces:
Serializable, Iterable<GeneSet>
public class GeneSetsRanked extends GeneSets
A collection of GeneSets Genes are ranked (usually by 'value')
Author:
Pablo Cingolani
See Also:

  • Constructor Details

    • GeneSetsRanked

      public GeneSetsRanked()
      Default constructor

    • GeneSetsRanked

      public GeneSetsRanked(GeneSets geneSets)

    • GeneSetsRanked

      public GeneSetsRanked(String msigDb)

  • Method Details

    • add

      public boolean add(String gene, int rank)
      Add a 'ranked' gene (to every corresponding GeneSet in this collection)
      Parameters:
      gene - : symbol's ID
      rank - : symbol's rank

    • checkInterestingGenes

      public void checkInterestingGenes(Set<String> intGenes)
      Checks that every symboolID is in the set (as 'interesting' genes)
      Overrides:
      checkInterestingGenes in class GeneSets
      Parameters:
      intGenes - : A set of interesting genes Throws an exception on error

    • getMaxRank

      public int getMaxRank()
      Get maximum rank
      Returns:

    • getRank

      public int getRank(String gene)
      Get gene's rank
      Parameters:
      gene -
      Returns:

    • getRankByGene

      public HashMap<String,Integer> getRankByGene()
      Get geneId <-> Rank mapping
      Returns:

    • getRankedSetsCount

      public int getRankedSetsCount()
      How many gene sets have ranked genes (i.e. rank sum > 0)
      Returns:
      Number of gene set such that rankSum > 0

    • isRanked

      public boolean isRanked()
      Overrides:
      isRanked in class GeneSets

    • isRanked

      public boolean isRanked(String geneName)

    • isUsed

      protected boolean isUsed(GeneSet gs)
      Is this gene set used? I.e. is there at least one gene 'used'? (e.g. interesting or ranked)
      Overrides:
      isUsed in class GeneSets
      Parameters:
      gs -
      Returns:

    • isUsed

      protected boolean isUsed(String geneName)
      Overrides:
      isUsed in class GeneSets

    • loadExperimentalValues

      public List<String> loadExperimentalValues(String fileName, boolean maskException)
      Reads a file with a list of genes and experimental values. Format: "gene \t value \n"
      Overrides:
      loadExperimentalValues in class GeneSets
      Parameters:
      fileName -
      Returns:
      A list of genes not found

    • rankByValue

      public int rankByValue(boolean orderAscending)
      Rank genes by value

    • reset

      public void reset()
      Reset every 'interesting' gene or ranked gene (on every single GeneSet in this GeneSets)
      Overrides:
      reset in class GeneSets