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"score<-,classicScore-method", "scoreOrder", "scoreOrder,classicScore-method" ] }, { "page": "dagFunctions", "title": "Utility functions to work with Directed Acyclic Graphs (DAG)", "topics": [ "buildLevels", "getGraphRoot", "getNoOfLevels", "reverseArch" ] }, { "page": "diagnosticMethods", "title": "Diagnostic functions for topGOdata and topGOresult objects.", "topics": [ "GenTable", "GenTable,topGOdata-method", "printGenes", "printGenes,topGOdata,character,character-method", "printGenes,topGOdata,character,missing-method", "printGenes-methods", "showGroupDensity" ] }, { "page": "elimCount-class", "title": "Classes \"elimCount\" and \"weight01Count\"", "topics": [ "contTable,elimCount-method", "cutOff", "cutOff,elimCount-method", "cutOff<-", "cutOff<-,elimCount-method", "depth", "depth,leaCount-method", "depth<-", "depth<-,leaCount-method", "elim", "elim,elimCount-method", "elim,weight01Count-method", "elim<-", "elim<-,elimCount-method", "elim<-,weight01Count-method", 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"initialize,weight01Expr-method", "leaExpr-class", "members,weight01Expr,missing-method", "numAllMembers,weight01Expr-method", "numMembers,weight01Expr-method", "weight01Expr-class" ] }, { "page": "elimScore-class", "title": "Classes \"elimScore\" and \"weight01Score\"", "topics": [ "allMembers,elimScore-method", "allMembers,weight01Score-method", "allScore,elimScore,logical-method", "allScore,elimScore,missing-method", "allScore,weight01Score,logical-method", "allScore,weight01Score,missing-method", "alternative,elimScore-method", "cutOff,elimScore-method", "cutOff<-,elimScore-method", "depth,leaScore-method", "depth<-,leaScore-method", "elim,elimScore-method", "elim,weight01Score-method", "elim<-,elimScore-method", "elim<-,weight01Score-method", "elimScore-class", "initialize,elimScore-method", "initialize,leaScore-method", "initialize,weight01Score-method", "leaScore-class", "members,elimScore-method", "members,weight01Score,missing-method", "membersScore,elimScore-method", "membersScore,weight01Score-method", "numAllMembers,elimScore-method", "numAllMembers,weight01Score-method", "numMembers,elimScore-method", "numMembers,weight01Score-method", "rankMembers,elimScore-method", "rankMembers,weight01Score-method", "score<-,elimScore-method", "weight01Score-class" ] }, { "page": "GOTests", "title": "Gene set tests statistics", "topics": [ "GOFisherTest", "GOglobalTest", "GOKSTest", "GOKSTiesTest", "GOSumTest", "GOtTest", "permSumStats", "permSumStats.all" ] }, { "page": "geneList", "title": "A toy example of a list of gene identifiers and the respective p-values", "topics": [ "affyLib", "geneList", "topDiffGenes" ] }, { "page": "getPvalues", "title": "Convenient function to compute p-values from a gene expression matrix.", "topics": [ "getPvalues" ] }, { "page": "getSigGroups", "title": "Interfaces for running the enrichment tests", "topics": [ "getSigGroups", "getSigGroups,topGOdata,classicCount-method", "getSigGroups,topGOdata,classicExpr-method", "getSigGroups,topGOdata,classicScore-method", "getSigGroups,topGOdata,elimCount-method", "getSigGroups,topGOdata,elimExpr-method", "getSigGroups,topGOdata,elimScore-method", "getSigGroups,topGOdata,leaCount-method", "getSigGroups,topGOdata,leaExpr-method", "getSigGroups,topGOdata,leaScore-method", "getSigGroups,topGOdata,parentChild-method", "getSigGroups,topGOdata,pC-method", "getSigGroups,topGOdata,weight01Count-method", "getSigGroups,topGOdata,weight01Expr-method", "getSigGroups,topGOdata,weight01Score-method", "getSigGroups,topGOdata,weightCount-method", "getSigGroups-methods", "runTest", "runTest,topGOdata,character,character-method", "runTest,topGOdata,missing,character-method", "whichAlgorithms", "whichTests" ] }, { "page": "GOdata", "title": "Sample topGOdata and topGOresult objects", "topics": [ "GOdata", "resultFisher", "resultKS" ] }, { "page": "groupGOTerms", "title": "Grouping of GO terms into the three ontologies", "topics": [ "GOBPTerm", "GOCCTerm", "GOMFTerm", "groupGOTerms" ] }, { "page": "groupStats-class", "title": "Class \"groupStats\"", "topics": [ "allMembers", "allMembers,groupStats-method", "allMembers<-", "allMembers<-,groupStats-method", "groupStats-class", "initialize,groupStats-method", "members", "members,groupStats,missing-method", "members<-", "members<-,groupStats-method", "Name", "Name,groupStats-method", "Name<-", "Name<-,groupStats-method", "numAllMembers", "numAllMembers,groupStats-method", "numMembers", "numMembers,groupStats-method", "runTest,groupStats,missing,missing-method", "runTest,groupStats-method", "testStatistic", "testStatistic,groupStats-method", "testStatPar", "testStatPar,groupStats-method", "updateGroup", "updateGroup,groupStats,character,character-method" ] }, { "page": "inducedGraph", "title": "The subgraph induced by a set of nodes.", "topics": [ "inducedGraph", "nodesInInducedGraph" ] }, { "page": "parentChild-class", "title": "Classes \"parentChild\" and \"pC\"", "topics": [ "allMembers,parentChild-method", "allMembers<-,parentChild-method", "allMembers<-,pC-method", "allParents", "allParents,parentChild-method", "initialize,parentChild-method", "initialize,pC-method", "joinFun", "joinFun,parentChild-method", "numAllMembers,parentChild-method", "numSigAll,parentChild-method", "parentChild-class", "pC-class", "sigAllMembers,parentChild-method", "sigMembers<-,parentChild-method", "sigMembers<-,pC-method", "updateGroup,parentChild,missing,character-method", "updateGroup,pC,missing,character-method", "updateGroup,pC,missing,missing-method" ] }, { "page": "printGraph-methods", "title": "Visualisation functions", "topics": [ "GOplot", "printGraph", "printGraph,topGOdata,topGOresult,numeric,missing-method", "printGraph,topGOdata,topGOresult,numeric,topGOresult-method", "printGraph-methods", "showSigOfNodes" ] }, { "page": "topGOdata-class", "title": "Class \"topGOdata\"", "topics": [ "allGenes", "allGenes,topGOdata-method", "attrInTerm", "attrInTerm,topGOdata,character,character-method", "attrInTerm,topGOdata,character,missing-method", "countGenesInTerm", "countGenesInTerm,topGOdata,character-method", "countGenesInTerm,topGOdata,missing-method", "description", "description,topGOdata-method", "description<-", "description<-,topGOdata,ANY-method", "expressionMatrix", "expressionMatrix,topGOdata-method", "feasible", "feasible,topGOdata-method", "feasible<-", "feasible<-,topGOdata-method", "genes", "genes,topGOdata-method", "geneScore", "geneScore,topGOdata,character-method", "geneScore,topGOdata,missing-method", "geneScore,topGOdata-method", "geneSelectionFun", "geneSelectionFun,topGOdata-method", "geneSelectionFun<-", "geneSelectionFun<-,topGOdata-method", "genesInTerm", "genesInTerm,topGOdata,character-method", "genesInTerm,topGOdata,missing-method", "graph", "graph,topGOdata-method", "graph<-", "graph<-,topGOdata-method", "initialize,topGOdata-method", "numGenes", "numGenes,topGOdata-method", "numSigGenes", "numSigGenes,topGOdata-method", "ontology", "ontology,topGOdata-method", "ontology<-", "ontology<-,topGOdata-method", "phenotype", "phenotype,topGOdata-method", "print,topGOdata-method", "scoresInTerm", "scoresInTerm,topGOdata,character-method", "scoresInTerm,topGOdata,missing-method", "show,topGOdata-method", "sigGenes", "sigGenes,topGOdata-method", "termStat", "termStat,topGOdata,character-method", "termStat,topGOdata,missing-method", "topGOdata-class", "updateGenes", "updateGenes,topGOdata,factor,missing-method", "updateGenes,topGOdata,numeric,function-method", "updateTerm<-", "updateTerm<-,topGOdata,character-method", "usedGO", "usedGO,topGOdata-method" ] }, { "page": "topGOresult-class", "title": "Class \"topGOresult\"", "topics": [ "algorithm", "algorithm,topGOresult-method", "algorithm<-", "algorithm<-,topGOresult-method", "combineResults", "description,topGOresult-method", "description<-,topGOresult,ANY-method", "geneData", "geneData,topGOresult-method", "geneData<-", "geneData<-,topGOresult-method", "initialize,topGOresult-method", "print,topGOresult-method", "score", "score,topGOresult-method", "score<-,topGOresult-method", "show,topGOresult-method", "testName", "testName,topGOresult-method", "testName<-", "testName<-,topGOresult-method", "topGOresult-class" ] }, { "page": "weightCount-class", "title": "Class \"weightCount\"", "topics": [ "allMembers,weightCount-method", "getSigRatio", "getSigRatio,weightCount-method", "initialize,weightCount-method", "members,weightCount-method", "Name,weightCount-method", "numAllMembers,weightCount-method", "numMembers,weightCount-method", "numSigAll,weightCount-method", "numSigMembers,weightCount-method", "penalise", "penalise,weightCount,numeric,numeric-method", "roundFun", "roundFun,weightCount-method", "significant", "significant,weightCount-method", "sigRatio", "sigRatio,weightCount-method", "sigRatio<-", "sigRatio<-,weightCount-method", "testStatistic,weightCount-method", "testStatPar,weightCount-method", "updateGroup,weightCount,character,character-method", "weightCount-class", "Weights", "Weights,weightCount,logical-method", "Weights,weightCount,missing-method", "Weights,weightCount-method", "Weights<-", "Weights<-,weightCount-method" ] } ], "_readme": "https://github.com/bioc/topGO/raw/HEAD/README.md", "_rundeps": [ "AnnotationDbi", "askpass", "Biobase", "BiocBaseUtils", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "fastmap", "generics", "glue", "GO.db", "graph", "httr", "IRanges", "jsonlite", "KEGGREST", "lattice", "lifecycle", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "SparseM", "sys", "vctrs", "XVector" ], "_vignettes": [ { "source": "topGO_manual.Rmd", "filename": "topGO_manual.html", "title": "Gene set enrichment analysis with topGO", "author": "Adrian Alexa, Jörg Rahnenführer, Federico Marini", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Quick start guide", "Data preparation", "Performing the enrichment tests", "Analysis of results", "The gene universe and the set of interesting genes", "The topGOdata object", "Custom annotations", "Predefined list of interesting genes", "Using the genes score", "Filtering and missing GO annotations", "Working with the topGOdata object", "Running the enrichment tests", "Defining and running the test", "The groupStats classes", "Performing the test", "The adjustment of $p$-values", "runTest: a high-level interface for testing", "Interpretation and visualization of results", "The topGOresult object", "Summarising the results", "Analysing individual GOs", "Visualising the GO structure", "Session Information", "References" ], "created": "2025-07-18 12:19:37", "modified": "2025-07-18 12:19:37", "commits": 1 } ], "_score": 11.127412921441458, "_indexed": true, "_nocasepkg": "topgo", "_universes": [ "bioc", "federicomarini" ], "_binaries": [ { "r": "4.7.0", 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