annotation | Accessors for HyperGResult Objects |
annotation,GOHyperGParams-method | Class "GOHyperGParams" |
annotation,HyperGParams-method | Class "HyperGParams" |
annotation,HyperGResultBase-method | Accessors for HyperGResult Objects |
applyByCategory | Apply a function to a vector of statistics, by category |
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" |
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 |
chrBandInciMat | Create an incidence matrix mapping chromosome bands to genes |
chrGraph | Accessors for HyperGResult Objects |
chrGraph,ChrMapHyperGResult-method | Accessors for HyperGResult Objects |
ChrMapHyperGParams-class | Class "ChrMapHyperGParams" |
ChrMapHyperGResult-class | Class "ChrMapHyperGResult" |
condGeneIdUniverse | Accessors for HyperGResult Objects |
condGeneIdUniverse,ChrMapHyperGResult-method | Accessors for HyperGResult Objects |
condGeneIdUniverse,HyperGResultBase-method | Accessors for HyperGResult Objects |
conditional | Class "HyperGParams" |
conditional,GOHyperGParams-method | Class "GOHyperGParams" |
conditional,HyperGParams-method | Class "HyperGParams" |
conditional<-,GOHyperGParams,logical-method | Class "GOHyperGParams" |
description | Accessors for HyperGResult Objects |
description,HyperGResultBase-method | Accessors for HyperGResult Objects |
expectedCounts | Accessors for HyperGResult Objects |
expectedCounts,ChrMapHyperGResult-method | Accessors for HyperGResult Objects |
expectedCounts,HyperGResult-method | Accessors for HyperGResult Objects |
findAMstats | Compute per category summary statistics |
geneCounts | Accessors for HyperGResult Objects |
geneCounts,HyperGResultBase-method | Accessors for HyperGResult Objects |
geneGoHyperGeoTest | Hypergeometric Tests for GO (DEFUNCT) |
geneIds | Accessors for HyperGResult Objects |
geneIds,HyperGParams-method | Class "HyperGParams" |
geneIds,HyperGResultBase-method | Accessors for HyperGResult Objects |
geneIds<-,HyperGParams,logical-method | Class "HyperGParams" |
geneIds<-,HyperGParams-method | Class "HyperGParams" |
geneIdsByCategory | Accessors for HyperGResult Objects |
geneIdsByCategory,HyperGResultBase-method | Accessors for HyperGResult Objects |
geneIdUniverse | Accessors for HyperGResult Objects |
geneIdUniverse,ChrMapHyperGResult-method | Accessors for HyperGResult Objects |
geneIdUniverse,HyperGResult-method | Accessors for HyperGResult Objects |
geneKeggHyperGeoTest | Hypergeometric Tests for KEGG (DEFUNCT) |
geneMappedCount | Accessors for HyperGResult Objects |
geneMappedCount,HyperGResultBase-method | Accessors for HyperGResult Objects |
getPathNames | A function to print pathway names given their numeric id. |
GOHyperGParams-class | Class "GOHyperGParams" |
htmlReport | Accessors for HyperGResult Objects |
htmlReport,HyperGResultBase-method | Accessors for HyperGResult Objects |
HyperGParams-class | Class "HyperGParams" |
HyperGResult-accessors | Accessors for HyperGResult Objects |
HyperGResult-class | Class "HyperGResult" |
HyperGResultBase-class | Class "HyperGResultBase" |
hyperGTest | Hypergeometric Test for association of categories and genes |
hyperGTest,ChrMapHyperGParams-method | Hypergeometric Test for association of categories and genes |
hyperGTest,HyperGParams-method | Hypergeometric Test for association of categories and genes |
initialize,HyperGParams-method | Class "HyperGParams" |
isConditional | Class "HyperGParams" |
isConditional,ChrMapHyperGResult-method | Accessors for HyperGResult Objects |
isConditional,HyperGParams-method | Class "HyperGParams" |
isConditional,HyperGResultBase-method | Accessors for HyperGResult Objects |
KEGGHyperGParams-class | Class "KEGGHyperGParams" and "PFAMHyperGParams" |
makeChrBandGraph | Create a graph representing chromosome band annotation data |
makeChrBandInciMat | Create an incidence matrix mapping chromosome bands to genes |
makeEBcontr | A function to make the contrast vectors needed for EBarrays |
makeValidParams | Non-standard Generic for Checking Validity of Parameter Objects |
makeValidParams,HyperGParams-method | Class "HyperGParams" |
MAPAmat | Create an adjacency matrix for MAP |
oddsRatios | Accessors for HyperGResult Objects |
oddsRatios,ChrMapHyperGResult-method | Accessors for HyperGResult Objects |
oddsRatios,HyperGResult-method | Accessors for HyperGResult Objects |
ontology | Class "HyperGParams" |
ontology,GOHyperGParams-method | Class "GOHyperGParams" |
ontology,HyperGParams-method | Class "HyperGParams" |
ontology<-,GOHyperGParams,character-method | Class "GOHyperGParams" |
PFAMHyperGParams-class | Class "KEGGHyperGParams" and "PFAMHyperGParams" |
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<-,HyperGParams-method | Class "HyperGParams" |
pvalues | Accessors for HyperGResult Objects |
pvalues,ChrMapHyperGResult-method | Accessors for HyperGResult Objects |
pvalues,HyperGResult-method | Accessors for HyperGResult Objects |
show,GOHyperGParams-method | Class "GOHyperGParams" |
show,HyperGParams-method | Class "HyperGParams" |
show,HyperGResultBase-method | Class "HyperGResultBase" |
sigCategories | Accessors for HyperGResult Objects |
sigCategories,HyperGResultBase-method | Accessors for HyperGResult Objects |
summary,HyperGResultBase-method | Accessors for HyperGResult Objects |
testDirection | Accessors for HyperGResult Objects |
testDirection,HyperGParams-method | Class "HyperGParams" |
testDirection,HyperGResultBase-method | Accessors for HyperGResult Objects |
testDirection<-,HyperGParams-method | Class "HyperGParams" |
testName | Accessors for HyperGResult Objects |
testName,HyperGResultBase-method | Accessors for HyperGResult Objects |
ttperm | A simple function to compute a permutation t-test. |
universeBuilder | Return a vector of gene identifiers with category annotations |
universeBuilder,GOHyperGParams-method | Return a vector of gene identifiers with category annotations |
universeBuilder,KEGGHyperGParams-method | Return a vector of gene identifiers with category annotations |
universeBuilder,PFAMHyperGParams-method | Return a vector of gene identifiers with category annotations |
universeCounts | Accessors for HyperGResult Objects |
universeCounts,HyperGResultBase-method | Accessors for HyperGResult Objects |
universeGeneIds | Class "HyperGParams" |
universeGeneIds,HyperGParams-method | Class "HyperGParams" |
universeMappedCount | Accessors for HyperGResult Objects |
universeMappedCount,HyperGResultBase-method | Accessors for HyperGResult Objects |