Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).
|Author||Robert M. Flight <firstname.lastname@example.org>|
|Date of publication||None|
|Maintainer||Robert M. Flight <email@example.com>|
breakEdges: Break Cytoscape (or graphNEL) Network Edges
breakEdges-methods: Methods for Function 'breakEdges' in Package...
categoryCompare-package: Meta-analysis of high-throughput experiments using feature...
ccCompare: Comparison of enriched annotations
ccCompareCollection-class: Class '"ccCompareCollection"'
ccCompareGeneric-methods: Methods for Function 'ccCompareGeneric' in Package...
ccCompareResult-class: Class '"ccCompareResult"'
ccData: Test data for 'categoryCompare'
ccEnrich: Perform annotation enrichment for multiple gene lists
ccEnrichCollection-class: Class "ccEnrichCollection"
ccEnrichResult-class: Class "ccEnrichResult"
ccGeneList-class: Class "ccGeneList"
ccOptions-class: Class "ccOptions"
ccOutCyt-methods: Methods for Function 'ccOutCyt' in Package 'categoryCompare'
ccSigList-class: Class '"ccSigList"'
cwReload-methods: Methods for Function 'cwReload' in Package 'categoryCompare'
cytOutData-methods: Methods for Function 'cytOutData'
cytOutNodes-methods: Methods for Function 'cytOutNodes'
fdr: Number of FDR runs to perform
GENccEnrichResult-class: Class '"GENccEnrichResult"'
getGeneSymbol: Entrez to name, symbol, GO and path conversion, as well as...
HyperGParamsCC-class: Class "HyperGParamsCC"
HyperGResultCC-class: Class "HyperGResultCC"
hyperGTestCC: Hypergeometric testing with false discovery rate
mergedData-class: Class '"mergedData"'
mergeLists-methods: Function 'mergeLists' in Package 'categoryCompare'
minNodes: Delete nodes with less than a certain number of genes...
pvalueType: Type of p-values to return from object
show-methods: Methods for Function show in Package 'categoryCompare'