# Meta-analysis of high-throughput experiments using feature annotations

## Documentation for package ‘categoryCompare’ version 1.54.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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"