Meta-analysis of high-throughput experiments using feature
annotations
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Documentation for package ‘categoryCompare’ version 1.49.0
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A B C E F G H K L M O P R S T misc
| categoryCompare-package | Meta-analysis of high-throughput experiments using feature annotations |
-- A --
| allAnnotation | Class '"ccCompareResult"' |
| allAnnotation-method | Class '"ccCompareResult"' |
| annotation-method | Class '"ccSigList"' |
-- B --
| breakEdges | Methods for Function 'breakEdges' in Package 'categoryCompare' |
| breakEdges-method | Methods for Function 'breakEdges' in Package 'categoryCompare' |
| breakEdges-methods | Methods for Function 'breakEdges' in Package 'categoryCompare' |
-- C --
| category-method | Class '"GENccEnrichResult"' |
| category-method | Class '"ccSigList"' |
| categoryCompare | Meta-analysis of high-throughput experiments using feature annotations |
| ccCompare | Comparison of enriched annotations |
| ccCompare-method | Comparison of enriched annotations |
| ccCompare-methods | Comparison of enriched annotations |
| ccCompareCollection | Class '"ccCompareCollection"' |
| ccCompareCollection-class | Class '"ccCompareCollection"' |
| ccCompareGeneric | Methods for Function 'ccCompareGeneric' in Package 'categoryCompare' |
| ccCompareGeneric-method | Class '"GENccEnrichResult"' |
| ccCompareGeneric-methods | Methods for Function 'ccCompareGeneric' in Package 'categoryCompare' |
| ccCompareResult | Class '"ccCompareResult"' |
| ccCompareResult-class | Class '"ccCompareResult"' |
| ccData | Test data for 'categoryCompare' |
| ccEnrich | Perform annotation enrichment for multiple gene lists |
| ccEnrich-method | Perform annotation enrichment for multiple gene lists |
| ccEnrichCollection | Class "ccEnrichCollection" |
| ccEnrichCollection-class | Class "ccEnrichCollection" |
| ccEnrichResult | Class "ccEnrichResult" |
| ccEnrichResult-class | Class "ccEnrichResult" |
| ccGeneList | Class "ccGeneList" |
| ccGeneList-class | Class "ccGeneList" |
| ccOptions | Class "ccOptions" |
| ccOptions-class | Class "ccOptions" |
| ccOptions-method | Methods for Function 'ccCompareGeneric' in Package 'categoryCompare' |
| ccOpts | Test data for 'categoryCompare' |
| ccOutCyt | Methods for Function 'ccOutCyt' in Package 'categoryCompare' |
| ccOutCyt-method | Methods for Function 'ccOutCyt' in Package 'categoryCompare' |
| ccOutCyt-methods | Methods for Function 'ccOutCyt' in Package 'categoryCompare' |
| ccResults | Test data for 'categoryCompare' |
| ccResultsBPHier | Test data for 'categoryCompare' |
| ccSigList | Class '"ccSigList"' |
| ccSigList-class | Class '"ccSigList"' |
| ccType | Class "ccGeneList" |
| ccType-method | Class "ccGeneList" |
| ccType<- | Class "ccGeneList" |
| ccType<--method | Class "ccGeneList" |
| compareColors | Class "ccOptions" |
| compareColors-method | Class "ccOptions" |
| compareColors<- | Class "ccOptions" |
| compareColors<--method | Class "ccOptions" |
| compareIndx | Class "ccOptions" |
| compareIndx-method | Class "ccOptions" |
| compareNames | Class "ccOptions" |
| compareNames-method | Class "ccOptions" |
| compareNames<- | Class "ccOptions" |
| compareNames<--method | Class "ccOptions" |
| cssClass | Class "ccOptions" |
| cssClass-method | Class "ccOptions" |
| cwReload | Methods for Function 'cwReload' in Package 'categoryCompare' |
| cwReload-method | Methods for Function 'cwReload' in Package 'categoryCompare' |
| cwReload-methods | Methods for Function 'cwReload' in Package 'categoryCompare' |
| cytOutData | Methods for Function 'cytOutData' |
| cytOutData-method | Methods for Function 'cytOutData' |
| cytOutData-methods | Methods for Function 'cytOutData' |
| cytOutNodes | Methods for Function 'cytOutNodes' |
| cytOutNodes-method | Methods for Function 'cytOutNodes' |
| cytOutNodes-methods | Methods for Function 'cytOutNodes' |
-- E --
| enrichLists | Test data for 'categoryCompare' |
-- F --
| fdr | Number of FDR runs to perform |
| fdr-method | Class "HyperGParamsCC" |
| fdr-method | Class "HyperGResultCC" |
| fdr-method | Class "ccEnrichResult" |
| fdr-method | Class "ccGeneList" |
| fdr<- | Number of FDR runs to perform |
| fdr<--method | Class "HyperGParamsCC" |
| fdr<--method | Class "ccGeneList" |
| fdrvalues | Class "HyperGResultCC" |
| fdrvalues-method | Class "HyperGResultCC" |
-- G --
| GENccEnrichResult | Class '"GENccEnrichResult"' |
| GENccEnrichResult-class | Class '"GENccEnrichResult"' |
| GENccEnrichResult-method | Methods for Function 'ccCompareGeneric' in Package 'categoryCompare' |
| geneAnnMapping | Class '"GENccEnrichResult"' |
| geneAnnMapping-method | Class '"GENccEnrichResult"' |
| geneLists | Test data for 'categoryCompare' |
| getAnnotation | Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion. |
| getGeneName | Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion. |
| getGeneSymbol | Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion. |
| getGO2ALLEGS | Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion. |
| getPATH2EG | Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion. |
| GOccEnrichResult | Class "ccEnrichResult" |
| GOccEnrichResult-class | Class "ccEnrichResult" |
| GOHyperGParams | Class "HyperGParamsCC" |
| GOHyperGParams-class | Class "HyperGParamsCC" |
| GOHyperGParamsCC | Class "HyperGParamsCC" |
| GOHyperGParamsCC-class | Class "HyperGParamsCC" |
| GOHyperGResultCC | Class "HyperGResultCC" |
| GOHyperGResultCC-class | Class "HyperGResultCC" |
| graphType | graphType |
| graphType-method | Class '"GENccEnrichResult"' |
| graphType-method | Class "ccEnrichCollection" |
| graphType-method | Class "ccEnrichResult" |
| graphType-methods | graphType |
| graphType<- | graphType |
| graphType<--method | Class '"GENccEnrichResult"' |
| graphType<--method | Class "ccEnrichCollection" |
| graphType<--method | Class "ccEnrichResult" |
| gseaRes | Test data for 'categoryCompare' |
| gUniverse | Test data for 'categoryCompare' |
-- H --
| HyperGParamsCC | Class "HyperGParamsCC" |
| HyperGParamsCC-class | Class "HyperGParamsCC" |
| HyperGResultCC | Class "HyperGResultCC" |
| HyperGResultCC-class | Class "HyperGResultCC" |
| hyperGTestCC | Hypergeometric testing with false discovery rate |
| hyperGTestCC,HyperGParamsCC | Hypergeometric testing with false discovery rate |
| hyperGTestCC-method | Hypergeometric testing with false discovery rate |
-- K --
| KEGGccEnrichResult | Class "ccEnrichResult" |
| KEGGccEnrichResult-class | Class "ccEnrichResult" |
| KEGGHyperGParams | Class "HyperGParamsCC" |
| KEGGHyperGParams-class | Class "HyperGParamsCC" |
| KEGGHyperGParamsCC | Class "HyperGParamsCC" |
| KEGGHyperGParamsCC-class | Class "HyperGParamsCC" |
| KEGGHyperGResultCC | Class "HyperGResultCC" |
| KEGGHyperGResultCC-class | Class "HyperGResultCC" |
-- L --
| listNames | listNames |
| listNames-method | Class "ccGeneList" |
| listNames-method | Class "ccOptions" |
| listNames<--method | Class "ccOptions" |
-- M --
| mainGraph | Class '"ccCompareResult"' |
| mainGraph-method | Class '"ccCompareResult"' |
| mainTable | Class '"ccCompareResult"' |
| mainTable-method | Class '"ccCompareResult"' |
| mergedData-class | Class '"mergedData"' |
| mergeLists | Function 'mergeLists' in Package 'categoryCompare' |
| mergeLists-method | Function 'mergeLists' in Package 'categoryCompare' |
| mergeLists-methods | Function 'mergeLists' in Package 'categoryCompare' |
| minCount | minCount |
| minCount-method | Class "HyperGResultCC" |
| minCount-method | Class "ccEnrichResult" |
| minCount<- | minCount |
| minCount<--method | Class "HyperGResultCC" |
| minCount<--method | Class "ccEnrichCollection" |
| minCount<--method | Class "ccEnrichResult" |
| minNodes | Delete nodes with less than a certain number of genes annotated |
| minNodes-method | Delete nodes with less than a certain number of genes annotated |
-- O --
| ontology-method | Class '"GENccEnrichResult"' |
| ontology-method | Class '"ccSigList"' |
| outType | Class "ccOptions" |
| outType-method | Class "ccOptions" |
| outType<- | Class "ccOptions" |
| outType<--method | Class "ccOptions" |
-- P --
| pCC-method | Class "HyperGResultCC" |
| pvalueCutoff-method | Class "ccEnrichResult" |
| pvalueCutoff-method | Class "ccGeneList" |
| pvalueCutoff<--method | Class "HyperGResultCC" |
| pvalueCutoff<--method | Class "ccEnrichCollection" |
| pvalueCutoff<--method | Class "ccEnrichResult" |
| pvalueCutoff<--method | Class "ccGeneList" |
| pvalueType | Type of p-values to return from object |
| pvalueType-method | Class "HyperGResultCC" |
| pvalueType-method | Class "ccEnrichResult" |
| pvalueType<- | Type of p-values to return from object |
| pvalueType<--method | Class "HyperGResultCC" |
| pvalueType<--method | Class "ccEnrichCollection" |
| pvalueType<--method | Class "ccEnrichResult" |
-- R --
| resetColors | resetColors |
| resetColors-method | resetColors |
| resetColors-methods | resetColors |
-- S --
| show-method | Methods for Function show in Package 'categoryCompare' |
| show-methods | Methods for Function show in Package 'categoryCompare' |
| sigID | Class '"GENccEnrichResult"' |
| sigID-method | Class '"ccSigList"' |
| summary-method | Methods for Function show in Package 'categoryCompare' |
| summary-methods | Methods for Function show in Package 'categoryCompare' |
-- T --
| table10 | Test data for 'categoryCompare' |
| table48 | Test data for 'categoryCompare' |
| testDirection-method | Class "ccGeneList" |
-- misc --
| [-method | Class '"GENccEnrichResult"' |
| [-method | Class "ccEnrichResult" |