edu.cmu.cs.sb.drem
Class DREM_GoAnnotations

java.lang.Object
  extended by edu.cmu.cs.sb.core.GoAnnotations
      extended by edu.cmu.cs.sb.drem.DREM_GoAnnotations

public class DREM_GoAnnotations
extends GoAnnotations

Class encapsules the Gene Ontology annotations and gene set enrichment functions used by DREM


Nested Class Summary
static class DREM_GoAnnotations.RecIDdrem
          A record for a GO category include ID, name, p-value based on a split, and a p-value overall
static class DREM_GoAnnotations.RecIDdremCompare
          Compares first by dpvalue (lower comes first) and then by dcategoryselect (greater comes first)
 
Nested classes/interfaces inherited from class edu.cmu.cs.sb.core.GoAnnotations
GoAnnotations.GORankingComparator, GoAnnotations.GoRec, GoAnnotations.GoResults, GoAnnotations.ProfileGORankingRec, GoAnnotations.Rec, GoAnnotations.RecCompare, GoAnnotations.RecCompareBinom, GoAnnotations.RecCount, GoAnnotations.RecIDpval, GoAnnotations.RecIDpval2
 
Field Summary
 DREM_GoAnnotations.RecIDdrem[] theRecIDdrem
           
 
Fields inherited from class edu.cmu.cs.sb.core.GoAnnotations
algoAll, algoAllbase, bactual, bcluster, bcontoval, bfontoval, bpontoval, brandomgoval, extragenes, extraprobes, goAll, htAlt, htAncestors, htFullCount, htGeneNames, htGO, htGoLabels, htIDCategory, nGeneSet, nlegalgo, nmaxsize, nmingo, nmingolevel, nsamplespval, numcategory, numtotalgenes, szcategoryIDval, szevidenceval, szextraval, szGoCategoryFile, szGoFile, szorganismsourceval, szSelectedGO, szsortcommand, sztaxonval, szxrefsourceval, szxrefval, theClusterRecIDpval, theRecIDpval, tpgr
 
Method Summary
 void buildRecDREM(edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode treeptr, java.lang.String[] genenames)
           
 void findmins(java.util.HashMap htGOtoMinSplit, java.util.HashMap htGOtoMinOverall, edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode treeptr, java.lang.String[] genenames, java.util.HashMap htParentGO)
          Determines the minimum overall and split p-values for each
 
Methods inherited from class edu.cmu.cs.sb.core.GoAnnotations
addgenesgo, addgenesgocategory, addOfficialLine, addprobegenemap, buildxref, computePValues, computePValues, computePValuesBase, containsTaxon, geneIsOfType, getCategory, getCategory, getCategory, getCategory, getgocategories, getLevel, hashtoList1, hashtoList2, incrementSelectData, isOrder, labelsForID, levelGO, loadID, loadIDbase, loadIDCategory, printLevel, updateBest, updateBestHyperBinom, validEvidence
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

theRecIDdrem

public DREM_GoAnnotations.RecIDdrem[] theRecIDdrem
Method Detail

buildRecDREM

public void buildRecDREM(edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode treeptr,
                         java.lang.String[] genenames)

findmins

public void findmins(java.util.HashMap htGOtoMinSplit,
                     java.util.HashMap htGOtoMinOverall,
                     edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode treeptr,
                     java.lang.String[] genenames,
                     java.util.HashMap htParentGO)
Determines the minimum overall and split p-values for each