Class LinkAnalysis


  • public class LinkAnalysis
    extends Object
    Handles the actual coexpression analysis, once handed data that has been prepared. Results are made available at the end. See LinkAnalysisCli for more instructions. This should be created for each analysis - it's not reusable.
    Author:
    xiangwan, paul (refactoring)
    • Field Detail

      • log

        protected static final org.apache.commons.logging.Log log
    • Method Detail

      • analyze

        public void analyze()
        Main entry point.
      • clear

        public void clear()
        Clear/null data so this object can be reused.
      • getAnalysisObj

        public CoexpressionAnalysis getAnalysisObj()
        Returns:
        object containing the parameters used.
      • getExpressionExperiment

        public BioAssaySet getExpressionExperiment()
      • setExpressionExperiment

        public void setExpressionExperiment​(BioAssaySet expressionExperiment)
      • getGenesTested

        public Set<Gene> getGenesTested()
        Gene the genes that were tested, according to the rows that are currently in the dataMatrix (so call this after filtering!)
        Returns:
        set
      • getProbeDegree

        public Integer getProbeDegree​(int index)
        Parameters:
        index - row number in the metrixMatirx
        Returns:
        how many Links that probe appears in, or null if the probeDegree has not been populated for that index (that is, either to early to check, or it was zero).
      • setProbeToGeneMap

        public void setProbeToGeneMap​(Map<CompositeSequence,​Set<Gene>> probeToGeneMap)
        Once set, is unmodifiable.
        Parameters:
        probeToGeneMap - map
      • getTaxon

        public Taxon getTaxon()
      • setTaxon

        public void setTaxon​(Taxon taxon)