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java.lang.Objectedu.cmu.cs.sb.core.GoAnnotations
edu.cmu.cs.sb.drem.DREM_GoAnnotations
public class DREM_GoAnnotations
Class encapsules the Gene Ontology annotations and gene set enrichment functions used by DREM
Nested Class Summary | |
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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 |
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GoAnnotations.GORankingComparator, GoAnnotations.GoRec, GoAnnotations.GoResults, GoAnnotations.ProfileGORankingRec, GoAnnotations.Rec, GoAnnotations.RecCompare, GoAnnotations.RecCompareBinom, GoAnnotations.RecCount, GoAnnotations.RecIDpval, GoAnnotations.RecIDpval2 |
Field Summary | |
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DREM_GoAnnotations.RecIDdrem[] |
theRecIDdrem
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Fields inherited from class edu.cmu.cs.sb.core.GoAnnotations |
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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 | |
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void |
buildRecDREM(edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode treeptr,
java.lang.String[] genenames)
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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 |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public DREM_GoAnnotations.RecIDdrem[] theRecIDdrem
Method Detail |
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public void buildRecDREM(edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode treeptr, java.lang.String[] genenames)
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)
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