Package org.snpeff.geneSets

Class GeneSetsRanked

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

    • Constructor Detail

      • GeneSetsRanked

        public GeneSetsRanked()
        Default constructor

      • GeneSetsRanked

        public GeneSetsRanked​(GeneSets geneSets)

      • GeneSetsRanked

        public GeneSetsRanked​(java.lang.String msigDb)

    • Method Detail

      • add

        public boolean add​(java.lang.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​(java.util.Set<java.lang.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​(java.lang.String gene)
        Get gene's rank
        Parameters:
        gene -
        Returns:

      • getRankByGene

        public java.util.HashMap<java.lang.String,​java.lang.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​(java.lang.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​(java.lang.String geneName)
        Overrides:
        isUsed in class GeneSets

      • loadExperimentalValues

        public java.util.List<java.lang.String> loadExperimentalValues​(java.lang.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