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Category Analysis

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37
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API for Category
Category Analysis

Global functions
. Man page
.GeneSetCollectionAnnotation Source code Source code
.createIdentityMap Source code
.doHyperGInternal Source code
.doHyperGTest Source code
.doLinearMTest Source code
.geneSetParamListFlip Source code
.getChildrenInGraph Source code
.hyperGTestInternal Source code
.linearMTestInternal Source code
.makeValidParams Source code
.replaceGOConditional Source code
.replaceGOOntology Source code
.setKeytype Source code
.strMatch Source code
AffyDatPkg-class Man page
ArabidopsisDatPkg-class Man page
Category-defunct Man page
ChrBandTree-class Man page
ChrBandTreeFromGraph Man page Source code
ChrMapHyperGParams-class Man page
ChrMapHyperGResult-class Man page
ChrMapLinearMParams-class Man page
ChrMapLinearMResult-class Man page
DatPkg-class Man page
DatPkgFactory Man page
DatPkgFactory,ChipDb-method Man page
DatPkgFactory,OBOCollection,GeneSetCollection-method Man page
DatPkgFactory,OrgDb-method Man page
DatPkgFactory,character-method Man page
GO2AllProbes Man page
GO2AllProbes,DatPkg-method Man page
GO2AllProbes,GeneSetCollectionDatPkg-method Man page
GO2AllProbes,Org.XX.egDatPkg-method Man page
GO2AllProbes,YeastDatPkg-method Man page
GOHyperGParams-class Man page
GSEAGOHyperGParams Man page Source code
GSEAKEGGHyperGParams Man page Source code
GeneSetCollectionDatPkg Man page Source code
HyperGParams-class Man page
HyperGResult-accessors Man page
HyperGResult-class Man page
HyperGResultBase-class Man page
ID2EntrezID Man page
ID2EntrezID,AffyDatPkg-method Man page
ID2EntrezID,ArabidopsisDatPkg-method Man page
ID2EntrezID,GeneSetCollectionDatPkg-method Man page
ID2EntrezID,Org.XX.egDatPkg-method Man page
ID2EntrezID,YeastDatPkg-method Man page
ID2GO Man page
ID2GO,DatPkg-method Man page
ID2GO,GeneSetCollectionDatPkg-method Man page
ID2KEGG Man page
ID2KEGG,DatPkg-method Man page
ID2KEGG,GeneSetCollectionDatPkg-method Man page
KEGG2AllProbes Man page
KEGG2AllProbes,DatPkg-method Man page
KEGG2AllProbes,GeneSetCollectionDatPkg-method Man page
KEGGHyperGParams-class Man page
KEGGHyperGResult-class Man page
LinearMParams-class Man page
LinearMResult-class Man page
LinearMResultBase-class Man page
MAPAmat Man page Source code
NewChrBandTree Man page Source code
OBOCollectionDatPkg Man page Source code
OBOCollectionDatPkg-class Man page
OBOHyperGParams Man page Source code
OBOHyperGParams-class Man page
Org.XX.egDatPkg-class Man page
PFAMHyperGParams-class Man page
PFAMHyperGResult-class Man page
XXX_getSummaryGeneric_XXX Source code
YeastDatPkg-class Man page
addChrBandAnnotation Source code
addHierarchyToIncidenceMatrix Source code
allGeneIds Man page
allGeneIds,ChrBandTree-method Man page
annBaseName Source code
annMapChooser Source code
ann_list_to_mat Source code
annotation Man page
annotation,GOHyperGParams-method Man page
annotation,HyperGParams-method Man page
annotation,HyperGResultBase-method Man page
annotation,LinearMParams-method Man page
annotation,LinearMResultBase-method Man page
annotation,OBOHyperGParams-method Man page
annotation<-,HyperGParams,character-method Man page
annotation<-,LinearMParams,character-method Man page
ans_acceptor_factory Source code
applyByCategory Man page Source code
augmentByAncestors Source code
augmentByAncestorsSmart Source code
bottomup_tree_visitor Man page Source code
cateGOry Man page Source code
categoryName Man page
categoryName,GOHyperGParams-method Man page
categoryName,HyperGParams-method Man page
categoryName,LinearMParams-method Man page
categoryName,OBOHyperGParams-method Man page
categoryToEntrezBuilder Man page
categoryToEntrezBuilder,GOHyperGParams-method Man page
categoryToEntrezBuilder,KEGGHyperGParams-method Man page
categoryToEntrezBuilder,OBOHyperGParams-method Man page
categoryToEntrezBuilder,PFAMHyperGParams-method Man page
cb_buildContinTable Source code
cb_buildInciMat Source code
cb_childAnnList Source code
cb_children Man page Source code
cb_contingency Man page Source code
cb_makeContinTable Source code
cb_parse_band_Hs Man page Source code
cb_parse_band_Mm Man page Source code
cb_parse_band_hsa Man page
cb_sigBands Man page Source code
cb_test Man page Source code
checkChrOrg Source code
childrenOf Man page
childrenOf,ChrBandTree,character-method Man page
chrBandInciMat Man page
chrGraph Man page
chrGraph,ChrMapHyperGResult-method Man page
chrGraph,ChrMapLinearMResult-method Man page
chrMap_hg_test Source code
cleanMapAndsOrs Source code
cleanMapAndsOrs_Hs Source code
cleanMapWeird Source code
cleanMapWeird_Hs Source code
cleanRanges Source code
cleanRanges_Hs Source code
cleanRanges_Mm Source code
condGeneIdUniverse Man page
conditional Man page
conditional,ChrMapHyperGParams-method Man page
conditional,ChrMapHyperGResult-method Man page
conditional,GOHyperGParams-method Man page
conditional,HyperGParams-method Man page
conditional,HyperGResultBase-method Man page
conditional,LinearMParams-method Man page
conditional,LinearMResultBase-method Man page
conditional,OBOHyperGParams-method Man page
conditional<- Man page
conditional<-,ChrMapHyperGParams,logical-method Man page
conditional<-,GOHyperGParams,logical-method Man page
conditional<-,LinearMParams,logical-method Man page
conditional<-,OBOHyperGParams,logical-method Man page
description Man page
description,HyperGResultBase-method Man page
description,LinearMResultBase-method Man page
effectSize Man page
effectSize,LinearMResult-method Man page
entrezGeneUniverse Source code
exampleLevels Man page Source code
expCounts Source code
expectedCounts Man page
expectedCounts,ChrMapHyperGResult-method Man page
expectedCounts,HyperGResult-method Man page
findAMstats Man page Source code
geneCounts Man page
geneCounts,HyperGResultBase-method Man page
geneGoHyperGeoTest Man page
geneIdUniverse Man page
geneIdUniverse,ChrMapHyperGResult-method Man page
geneIdUniverse,HyperGResult-method Man page
geneIdUniverse,LinearMResultBase-method Man page
geneIds Man page
geneIds,ChrBandTree-method Man page
geneIds,HyperGParams-method Man page
geneIds,HyperGResultBase-method Man page
geneIds,LinearMParams-method Man page
geneIds,LinearMResultBase-method Man page
geneIds<- Man page
geneIds<-,HyperGParams,ANY-method Man page
geneIds<-,HyperGParams,logical-method Man page
geneIds<-,LinearMParams,ANY-method Man page
geneIdsByCategory Man page
geneIdsByCategory,HyperGResultBase-method Man page
geneIdsByCategory,LinearMResultBase-method Man page
geneKeggHyperGeoTest Man page
geneMappedCount Man page Man page
geneMappedCount,HyperGResultBase-method Man page
geneMappedCount,LinearMResultBase-method Man page
getDataEnv Source code
getDbAnnMap Source code
getGoToEntrezMap Source code
getGoToEntrezMap_db Source code
getGoToProbeMap Source code
getKeggToEntrezMap Source code
getKeggToProbeMap Source code
getOrganism Source code
getPathNames Man page Source code
getPfamToEntrezMap Source code
getPfamToProbeMap Source code
getUniverseHelper Source code
getUniverseViaGo Source code
getUniverseViaKegg Source code
getUniverseViaKegg_db Source code
getUniverseViaPfam Source code
getUniverseViaPfam_db Source code
getWantedResults Source code
global_ndummy Source code
global_tdummy Source code
gseattperm Man page Source code
hg_test_factory Man page Source code
htmlReport Man page
htmlReport,HyperGResultBase-method Man page
htmlReport,KEGGHyperGResult-method Man page
htmlReport,PFAMHyperGResult-method Man page
htmlReportFromDf Source code
hyperGTest Man page
hyperGTest,ChrMapHyperGParams-method Man page
hyperGTest,HyperGParams-method Man page
hyperGTest,KEGGHyperGParams-method Man page
hyperGTest,PFAMHyperGParams-method Man page
hyperg Man page
hyperg,character-method Man page
hyperg,list-method Man page
initialize,HyperGParams-method Man page
isConditional Man page
isDBDatPkg,DatPkg-method Man page
isDBDatPkg,GeneSetCollectionDatPkg-method Man page
level2nodes Man page
level2nodes,ChrBandTree,character-method Man page
level2nodes,ChrBandTree,numeric-method Man page
lgeneIds Man page
lgeneIds,ChrBandTree-method Man page
linearMEffectSizeMarginal Source code
linearMTest Man page
linearMTest,ChrMapLinearMParams-method Man page
linearMTest,LinearMParams-method Man page
linearMTestMarginal Source code
local_tdummy Source code
local_test_factory Man page Source code
makeChrBandGSC Man page Source code
makeChrBandGraph Man page Source code
makeChrBandInciMat Man page Source code
makeChrMapToEntrez Source code
makeContinTable Source code
makeEBcontr Man page Source code
makeValidParams Man page
makeValidParams,HyperGParams-method Man page
make_hyperg_result Source code
make_level2node_map Source code
oddsRatios Man page
oddsRatios,ChrMapHyperGResult-method Man page
oddsRatios,HyperGResult-method Man page
ontology Man page
ontology,GOHyperGParams-method Man page
ontology,HyperGParams-method Man page
ontology<- Man page
ontology<-,GOHyperGParams,character-method Man page
organism,DatPkg-method Man page
organism,GeneSetCollectionDatPkg-method Man page
organism,HyperGParams-method Man page
organism,HyperGResult-method Man page
parentOf Man page
parentOf,ChrBandTree,character-method Man page
probeToEntrezMapHelper Source code
probes2MAP Man page
probes2Path Man page Source code
pvalFromPermMat Source code
pvalueCutoff Man page
pvalueCutoff,HyperGParams-method Man page
pvalueCutoff,HyperGResultBase-method Man page
pvalueCutoff,LinearMParams-method Man page
pvalueCutoff,LinearMResultBase-method Man page
pvalueCutoff<- Man page
pvalueCutoff<-,HyperGParams-method Man page
pvalueCutoff<-,LinearMParams-method Man page
pvalues Man page
pvalues,ChrMapHyperGResult-method Man page
pvalues,HyperGResult-method Man page
pvalues,LinearMResult-method Man page
qRequire Source code
removeLengthZero Source code
removeLengthZeroAndMissing Source code
removeSigKidGenes Source code
show,ChrBandTree-method Man page
show,GOHyperGParams-method Man page
show,HyperGParams-method Man page
show,HyperGResultBase-method Man page
show,LinearMParams-method Man page
show,LinearMResultBase-method Man page
show,OBOHyperGParams-method Man page
sigCategories Man page
sigCategories,HyperGResultBase-method Man page
sigCategories,LinearMResultBase-method Man page
simple_acceptor Source code
splitOrfByPfam Source code
summary,HyperGResultBase-method Man page
summary,KEGGHyperGResult-method Man page
summary,LinearMResult-method Man page
summary,LinearMResultBase-method Man page
summary,PFAMHyperGResult-method Man page
testDirection Man page
testDirection,HyperGParams-method Man page
testDirection,HyperGResultBase-method Man page
testDirection,LinearMParams-method Man page
testDirection,LinearMResultBase-method Man page
testDirection<- Man page
testDirection<-,HyperGParams-method Man page
testDirection<-,LinearMParams-method Man page
testName Man page
testName,HyperGResultBase-method Man page
testName,LinearMResultBase-method Man page
toDF Source code
topdown_tree_visitor Man page Source code
treeLevels Man page
treeLevels,ChrBandTree-method Man page
tree_visitor Man page Source code
ttperm Man page Source code
universeBuilder Man page
universeBuilder,GOHyperGParams-method Man page
universeBuilder,KEGGHyperGParams-method Man page
universeBuilder,OBOHyperGParams-method Man page
universeBuilder,PFAMHyperGParams-method Man page
universeCounts Man page
universeCounts,HyperGResultBase-method Man page
universeCounts,LinearMResultBase-method Man page
universeGeneIds Man page
universeGeneIds,HyperGParams-method Man page
universeGeneIds,LinearMParams-method Man page
universeMappedCount Man page
universeMappedCount,HyperGResultBase-method Man page
universeMappedCount,LinearMResultBase-method Man page
Category documentation built on Nov. 8, 2020, 10:58 p.m.

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