annotation,GOHyperGParams-method |
Class "GOHyperGParams" |
annotation,HyperGParams-method |
Class "HyperGParams" |
annotation,HyperGResultBase-method |
Class "HyperGResultBase" |
applyByCategory |
Apply a function to a vector of statistics, by category |
cateGOry |
Construct a category membership data structure 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 |
conditional |
Class "HyperGParams" |
conditional,GOHyperGParams-method |
Class "GOHyperGParams" |
conditional,HyperGParams-method |
Class "HyperGParams" |
conditional<-,GOHyperGParams,logical-method |
Class "GOHyperGParams" |
description,HyperGResultBase-method |
Class "HyperGResultBase" |
expectedCounts |
Class "HyperGResult" |
expectedCounts,HyperGResult-method |
Class "HyperGResult" |
findAMstats |
Compute per category summary statistics |
geneCounts |
Class "HyperGResult" |
geneCounts,HyperGResult-method |
Class "HyperGResult" |
geneGoHyperGeoTest |
Hypergeometric Tests for GO |
geneIds |
Class "HyperGResultBase" |
geneIds,HyperGParams-method |
Class "HyperGParams" |
geneIds,HyperGResultBase-method |
Class "HyperGResultBase" |
geneIds<-,HyperGParams,logical-method |
Class "HyperGParams" |
geneIds<-,HyperGParams-method |
Class "HyperGParams" |
geneKeggHyperGeoTest |
Hypergeometric Tests for KEGG |
geneMappedCount |
Class "HyperGResultBase" |
geneMappedCount,HyperGResultBase-method |
Class "HyperGResultBase" |
getPathNames |
A function to print pathway names given their numeric id. |
GOHyperGParams-class |
Class "GOHyperGParams" |
htmlReport |
Class "HyperGResultBase" |
htmlReport,HyperGResultBase-method |
Class "HyperGResultBase" |
HyperGParams-class |
Class "HyperGParams" |
HyperGResult-class |
Class "HyperGResult" |
HyperGResultBase-class |
Class "HyperGResultBase" |
hyperGTest |
Hypergeometric Test for association of categories and genes |
hyperGTest,HyperGParams-method |
Hypergeometric Test for association of categories and genes |
isConditional |
Class "HyperGParams" |
isConditional,HyperGParams-method |
Class "HyperGParams" |
isConditional,HyperGResultBase-method |
Class "HyperGResultBase" |
KEGGHyperGParams-class |
Class "KEGGHyperGParams" and "PFAMHyperGParams" |
makeEBcontr |
A function to make the contrast vectors needed for EBarrays |
MAPAmat |
Create an adjacency matrix for MAP |
oddsRatios |
Class "HyperGResult" |
oddsRatios,HyperGResult-method |
Class "HyperGResult" |
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 |
Class "HyperGResultBase" |
pvalueCutoff,HyperGParams-method |
Class "HyperGParams" |
pvalueCutoff,HyperGResultBase-method |
Class "HyperGResultBase" |
pvalueCutoff<-,HyperGParams-method |
Class "HyperGParams" |
pvalues |
Class "HyperGResult" |
pvalues,HyperGResult-method |
Class "HyperGResult" |
show,GOHyperGParams-method |
Class "GOHyperGParams" |
show,HyperGResultBase-method |
Class "HyperGResultBase" |
summary,HyperGResultBase-method |
Class "HyperGResultBase" |
testDirection |
Class "HyperGResultBase" |
testDirection,HyperGParams-method |
Class "HyperGParams" |
testDirection,HyperGResultBase-method |
Class "HyperGResultBase" |
testDirection<-,HyperGParams-method |
Class "HyperGParams" |
testName |
Class "HyperGResultBase" |
testName,HyperGResultBase-method |
Class "HyperGResultBase" |
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 |
Class "HyperGResult" |
universeCounts,HyperGResult-method |
Class "HyperGResult" |
universeGeneIds |
Class "HyperGParams" |
universeGeneIds,HyperGParams-method |
Class "HyperGParams" |
universeMappedCount |
Class "HyperGResult" |
universeMappedCount,HyperGResult-method |
Class "HyperGResult" |