cateGOry |
Construct a category membership matrix from a list of gene
identifiers and their annotated GO categories. |
categoryName |
Class "HyperGParams" |
categoryName,GOHyperGParams-method |
Class "GOHyperGParams" |
categoryName,HyperGParams-method |
Class "HyperGParams" |
categoryName,LinearMParams-method |
Class "LinearMParams" |
categoryToEntrezBuilder |
Return a list mapping category ids to Entrez Gene ids |
categoryToEntrezBuilder,GOHyperGParams-method |
Return a list mapping category ids to Entrez Gene ids |
categoryToEntrezBuilder,KEGGHyperGParams-method |
Return a list mapping category ids to Entrez Gene ids |
categoryToEntrezBuilder,PFAMHyperGParams-method |
Return a list mapping category ids to Entrez Gene ids |
cb_children |
Create and Test Contingency Tables of Chromosome Band Annotations |
cb_contingency |
Create and Test Contingency Tables of Chromosome Band Annotations |
cb_parse_band_Hs |
Parse Homo Sapiens Chromosome Band Annotations |
cb_parse_band_hsa |
Parse Homo Sapiens Chromosome Band Annotations |
cb_parse_band_Mm |
Parse Mus Musculus Chromosome Band Annotations |
cb_sigBands |
Create and Test Contingency Tables of Chromosome Band Annotations |
cb_test |
Chromosome Band Tree-Based Hypothesis Testing |
childrenOf |
Class "ChrBandTree" |
childrenOf,ChrBandTree,character-method |
Class "ChrBandTree" |
chrBandInciMat |
Create an incidence matrix mapping chromosome bands to genes |
ChrBandTree-class |
Class "ChrBandTree" |
ChrBandTreeFromGraph |
Create a new ChrBandTree object |
chrGraph |
Accessors for HyperGResult Objects |
chrGraph,ChrMapHyperGResult-method |
Accessors for HyperGResult Objects |
chrGraph,ChrMapLinearMResult-method |
Class "ChrMapLinearMResult" |
ChrMapHyperGParams-class |
Class "ChrMapHyperGParams" |
ChrMapHyperGResult-class |
Class "ChrMapHyperGResult" |
ChrMapLinearMParams-class |
Class "ChrMapLinearMParams" |
ChrMapLinearMResult-class |
Class "ChrMapLinearMResult" |
condGeneIdUniverse |
Accessors for HyperGResult Objects |
condGeneIdUniverse,ChrMapHyperGResult-method |
Accessors for HyperGResult Objects |
condGeneIdUniverse,ChrMapLinearMResult-method |
Class "ChrMapLinearMResult" |
condGeneIdUniverse,HyperGResultBase-method |
Accessors for HyperGResult Objects |
condGeneIdUniverse,LinearMResultBase-method |
Class "LinearMResultBase" |
conditional |
Class "HyperGParams" |
conditional,ChrMapHyperGParams-method |
Class "ChrMapHyperGParams" |
conditional,ChrMapHyperGResult-method |
Class "ChrMapHyperGResult" |
conditional,ChrMapLinearMParams-method |
Class "ChrMapLinearMParams" |
conditional,GOHyperGParams-method |
Class "GOHyperGParams" |
conditional,HyperGParams-method |
Class "HyperGParams" |
conditional,HyperGResultBase-method |
Class "HyperGResultBase" |
conditional,LinearMParams-method |
Class "LinearMParams" |
conditional,LinearMResultBase-method |
Class "LinearMResultBase" |
conditional<- |
Class "HyperGParams" |
conditional<-,ChrMapHyperGParams,logical-method |
Class "ChrMapHyperGParams" |
conditional<-,ChrMapLinearMParams,logical-method |
Class "ChrMapLinearMParams" |
conditional<-,GOHyperGParams,logical-method |
Class "GOHyperGParams" |
geneCounts |
Accessors for HyperGResult Objects |
geneCounts,HyperGResultBase-method |
Accessors for HyperGResult Objects |
geneGoHyperGeoTest |
Hypergeometric Tests for GO (DEFUNCT) |
geneIds |
Accessors for HyperGResult Objects |
geneIds,ChrBandTree-method |
Class "ChrBandTree" |
geneIds,HyperGParams-method |
Class "HyperGParams" |
geneIds,HyperGResultBase-method |
Accessors for HyperGResult Objects |
geneIds,LinearMParams-method |
Class "LinearMParams" |
geneIds,LinearMResultBase-method |
Class "LinearMResultBase" |
geneIds<- |
Class "HyperGParams" |
geneIds<-,HyperGParams,ANY-method |
Class "HyperGParams" |
geneIds<-,HyperGParams,logical-method |
Class "HyperGParams" |
geneIds<-,LinearMParams,ANY-method |
Class "LinearMParams" |
geneIdsByCategory |
Accessors for HyperGResult Objects |
geneIdsByCategory,HyperGResultBase-method |
Accessors for HyperGResult Objects |
geneIdsByCategory,LinearMResultBase-method |
Class "LinearMResultBase" |
geneIdUniverse |
Accessors for HyperGResult Objects |
geneIdUniverse,ChrMapHyperGResult-method |
Accessors for HyperGResult Objects |
geneIdUniverse,HyperGResult-method |
Accessors for HyperGResult Objects |
geneIdUniverse,LinearMResult-method |
Class "LinearMResult" |
geneKeggHyperGeoTest |
Hypergeometric Tests for KEGG (DEFUNCT) |
geneMappedCount |
Accessors for HyperGResult Objects |
geneMappedCount,HyperGResultBase-method |
Accessors for HyperGResult Objects |
geneMappedCount,LinearMResultBase-method |
Class "LinearMResultBase" |
GeneSetCollectionDatPkg |
Class "DatPkg" |
getPathNames |
A function to print pathway names given their numeric ID. |
GO2AllProbes |
Class "DatPkg" |
GO2AllProbes,DatPkg-method |
Class "DatPkg" |
GO2AllProbes,GeneSetCollectionDatPkg-method |
Class "DatPkg" |
GO2AllProbes,Org.XX.egDatPkg-method |
Class "DatPkg" |
GO2AllProbes,YeastDatPkg-method |
Class "DatPkg" |
GOHyperGParams-class |
Class "GOHyperGParams" |
GSEAGOHyperGParams |
Helper function for constructing a GOHyperGParams objects or
KEGGHyperGParams objects from a GeneSetCollection |
GSEAKEGGHyperGParams |
Helper function for constructing a GOHyperGParams objects or
KEGGHyperGParams objects from a GeneSetCollection |
gseattperm |
Permutation p-values for GSEA |
ID2EntrezID |
Class "DatPkg" |
ID2EntrezID,AffyDatPkg-method |
Class "DatPkg" |
ID2EntrezID,ArabidopsisDatPkg-method |
Class "DatPkg" |
ID2EntrezID,GeneSetCollectionDatPkg-method |
Class "DatPkg" |
ID2EntrezID,Org.XX.egDatPkg-method |
Class "DatPkg" |
ID2EntrezID,YeastDatPkg-method |
Class "DatPkg" |
ID2GO |
Class "DatPkg" |
ID2GO,DatPkg-method |
Class "DatPkg" |
ID2GO,GeneSetCollectionDatPkg-method |
Class "DatPkg" |
ID2KEGG |
Class "DatPkg" |
ID2KEGG,DatPkg-method |
Class "DatPkg" |
ID2KEGG,GeneSetCollectionDatPkg-method |
Class "DatPkg" |
initialize,HyperGParams-method |
Class "HyperGParams" |
isConditional |
Class "HyperGParams" |
isConditional,ChrMapHyperGParams-method |
Class "ChrMapHyperGParams" |
isConditional,ChrMapHyperGResult-method |
Accessors for HyperGResult Objects |
isConditional,ChrMapLinearMResult-method |
Class "ChrMapLinearMResult" |
isConditional,GOHyperGParams-method |
Class "GOHyperGParams" |
isConditional,HyperGParams-method |
Class "HyperGParams" |
isConditional,HyperGResultBase-method |
Accessors for HyperGResult Objects |
isConditional,LinearMResultBase-method |
Class "LinearMResultBase" |
isDBDatPkg,DatPkg-method |
Class "DatPkg" |
isDBDatPkg,GeneSetCollectionDatPkg-method |
Class "DatPkg" |
parentOf |
Class "ChrBandTree" |
parentOf,ChrBandTree,character-method |
Class "ChrBandTree" |
PFAMHyperGParams-class |
Class "KEGGHyperGParams" and "PFAMHyperGParams" |
PFAMHyperGResult-class |
Class "HyperGResult" |
probes2MAP |
Map probe IDs to MAP regions. |
probes2Path |
A function to map probe identifiers to pathways. |
pvalueCutoff |
Accessors for HyperGResult Objects |
pvalueCutoff,HyperGParams-method |
Class "HyperGParams" |
pvalueCutoff,HyperGResultBase-method |
Accessors for HyperGResult Objects |
pvalueCutoff,LinearMParams-method |
Class "LinearMParams" |
pvalueCutoff,LinearMResultBase-method |
Class "LinearMResultBase" |
pvalueCutoff<- |
Class "HyperGParams" |
pvalueCutoff<-,HyperGParams-method |
Class "HyperGParams" |
pvalueCutoff<-,LinearMParams-method |
Class "LinearMParams" |
pvalues |
Accessors for HyperGResult Objects |
pvalues,ChrMapHyperGResult-method |
Accessors for HyperGResult Objects |
pvalues,HyperGResult-method |
Accessors for HyperGResult Objects |
pvalues,LinearMResult-method |
Class "LinearMResult" |
show,ChrBandTree-method |
Class "ChrBandTree" |
show,GOHyperGParams-method |
Class "GOHyperGParams" |
show,HyperGParams-method |
Class "HyperGParams" |
show,HyperGResultBase-method |
Class "HyperGResultBase" |
show,LinearMParams-method |
Class "LinearMParams" |
show,LinearMResultBase-method |
Class "LinearMResultBase" |
sigCategories |
Accessors for HyperGResult Objects |
sigCategories,HyperGResultBase-method |
Accessors for HyperGResult Objects |
sigCategories,LinearMResultBase-method |
Class "LinearMResultBase" |
summary,HyperGResultBase-method |
Accessors for HyperGResult Objects |
summary,KEGGHyperGResult-method |
Accessors for HyperGResult Objects |
summary,LinearMResultBase-method |
Class "LinearMResultBase" |
summary,PFAMHyperGResult-method |
Accessors for HyperGResult Objects |