Category Analysis
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Documentation for package ‘Category’ version 2.64.0
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A C D E F G H I K L M N O P S T U Y
-- A --
| AffyDatPkg-class | Class "DatPkg" |
| allGeneIds | Class "ChrBandTree" |
| allGeneIds-method | Class "ChrBandTree" |
| annotation | Accessors for HyperGResult Objects |
| annotation-method | Class "GOHyperGParams" |
| annotation-method | Class "HyperGParams" |
| annotation-method | Accessors for HyperGResult Objects |
| annotation-method | Class "LinearMParams" |
| annotation-method | Class "LinearMResultBase" |
| annotation-method | Class "OBOHyperGParams" |
| annotation<--method | Class "HyperGParams" |
| annotation<--method | Class "LinearMParams" |
| applyByCategory | Apply a function to a vector of statistics, by category |
| ArabidopsisDatPkg-class | Class "DatPkg" |
-- C --
| cateGOry | Construct a category membership matrix from a list of gene identifiers and their annotated GO categories. |
| Category-defunct | Defunct Functions in Package 'Category' |
| categoryName | Class "HyperGParams" |
| categoryName-method | Class "GOHyperGParams" |
| categoryName-method | Class "HyperGParams" |
| categoryName-method | Class "LinearMParams" |
| categoryName-method | Class "OBOHyperGParams" |
| categoryToEntrezBuilder | Return a list mapping category ids to Entrez Gene ids |
| categoryToEntrezBuilder-method | Return a list mapping category ids to Entrez Gene ids |
| cb_children | Create and Test Contingency Tables of Chromosome Band Annotations |
| cb_contingency | Create and Test Contingency Tables of Chromosome Band Annotations |
| cb_parse_band_Hs | Parse Homo Sapiens Chromosome Band Annotations |
| cb_parse_band_hsa | Defunct Functions in Package 'Category' |
| cb_parse_band_Mm | Parse Mus Musculus Chromosome Band Annotations |
| cb_sigBands | Create and Test Contingency Tables of Chromosome Band Annotations |
| cb_test | Chromosome Band Tree-Based Hypothesis Testing |
| childrenOf | Class "ChrBandTree" |
| childrenOf-method | Class "ChrBandTree" |
| chrBandInciMat | Defunct Functions in Package 'Category' |
| ChrBandTree-class | Class "ChrBandTree" |
| ChrBandTreeFromGraph | Create a new ChrBandTree object |
| chrGraph | Accessors for HyperGResult Objects |
| chrGraph-method | Class "ChrMapLinearMResult" |
| chrGraph-method | Accessors for HyperGResult Objects |
| ChrMapHyperGParams-class | Class "ChrMapHyperGParams" |
| ChrMapHyperGResult-class | Class "ChrMapHyperGResult" |
| ChrMapLinearMParams-class | Class "ChrMapLinearMParams" |
| ChrMapLinearMResult-class | Class "ChrMapLinearMResult" |
| condGeneIdUniverse | Defunct Functions in Package 'Category' |
| conditional | Class "HyperGParams" |
| conditional-method | Class "ChrMapHyperGParams" |
| conditional-method | Class "ChrMapHyperGResult" |
| conditional-method | Class "GOHyperGParams" |
| conditional-method | Class "HyperGParams" |
| conditional-method | Class "HyperGResultBase" |
| conditional-method | Class "LinearMParams" |
| conditional-method | Class "LinearMResultBase" |
| conditional-method | Class "OBOHyperGParams" |
| conditional<- | Class "HyperGParams" |
| conditional<--method | Class "ChrMapHyperGParams" |
| conditional<--method | Class "GOHyperGParams" |
| conditional<--method | Class "LinearMParams" |
| conditional<--method | Class "OBOHyperGParams" |
-- D --
| DatPkg-class | Class "DatPkg" |
| DatPkgFactory | Class "DatPkg" |
| DatPkgFactory-method | Class "DatPkg" |
| description | Accessors for HyperGResult Objects |
| description-method | Accessors for HyperGResult Objects |
| description-method | Class "LinearMResultBase" |
-- E --
| effectSize | Extract estimated effect sizes |
| effectSize-method | Class "LinearMResult" |
| exampleLevels | Display a sample node from each level of a ChrBandTree object |
| expectedCounts | Accessors for HyperGResult Objects |
| expectedCounts-method | Accessors for HyperGResult Objects |
-- F --
| findAMstats | Compute per category summary statistics |
-- G --
| geneCounts | Accessors for HyperGResult Objects |
| geneCounts-method | Accessors for HyperGResult Objects |
| geneGoHyperGeoTest | Defunct Functions in Package 'Category' |
| geneIds | Accessors for HyperGResult Objects |
| geneIds-method | Class "ChrBandTree" |
| geneIds-method | Class "HyperGParams" |
| geneIds-method | Accessors for HyperGResult Objects |
| geneIds-method | Class "LinearMParams" |
| geneIds-method | Class "LinearMResultBase" |
| geneIds<- | Class "HyperGParams" |
| geneIds<--method | Class "HyperGParams" |
| geneIds<--method | Class "LinearMParams" |
| geneIdsByCategory | Accessors for HyperGResult Objects |
| geneIdsByCategory-method | Accessors for HyperGResult Objects |
| geneIdsByCategory-method | Class "LinearMResultBase" |
| geneIdUniverse | Accessors for HyperGResult Objects |
| geneIdUniverse-method | Accessors for HyperGResult Objects |
| geneIdUniverse-method | Class "LinearMResultBase" |
| geneKeggHyperGeoTest | Defunct Functions in Package 'Category' |
| geneMappedCount | Accessors for HyperGResult Objects |
| geneMappedCount-method | Accessors for HyperGResult Objects |
| geneMappedCount-method | Class "LinearMResultBase" |
| GeneSetCollectionDatPkg | Class "DatPkg" |
| getPathNames | A function to print pathway names given their numeric ID. |
| GO2AllProbes | Class "DatPkg" |
| GO2AllProbes-method | Class "DatPkg" |
| GOHyperGParams-class | Class "GOHyperGParams" |
| GSEAGOHyperGParams | Helper function for constructing a GOHyperGParams objects or KEGGHyperGParams objects from a GeneSetCollection |
| GSEAKEGGHyperGParams | Helper function for constructing a GOHyperGParams objects or KEGGHyperGParams objects from a GeneSetCollection |
| gseattperm | Permutation p-values for GSEA |
-- H --
| htmlReport | Accessors for HyperGResult Objects |
| htmlReport-method | Accessors for HyperGResult Objects |
| hyperg | Hypergeometric (gene set enrichment) tests on character vectors. |
| hyperg-method | Hypergeometric (gene set enrichment) tests on character vectors. |
| HyperGParams-class | Class "HyperGParams" |
| HyperGResult-accessors | Accessors for HyperGResult Objects |
| HyperGResult-class | Class "HyperGResult" |
| HyperGResultBase-class | Class "HyperGResultBase" |
| hyperGTest | Hypergeometric Test for association of categories and genes |
| hyperGTest-method | Hypergeometric Test for association of categories and genes |
-- I --
| ID2EntrezID | Class "DatPkg" |
| ID2EntrezID-method | Class "DatPkg" |
| ID2GO | Class "DatPkg" |
| ID2GO-method | Class "DatPkg" |
| ID2KEGG | Class "DatPkg" |
| ID2KEGG-method | Class "DatPkg" |
| initialize-method | Class "HyperGParams" |
| isConditional | Defunct Functions in Package 'Category' |
| isDBDatPkg-method | Class "DatPkg" |
-- K --
| KEGG2AllProbes | Class "DatPkg" |
| KEGG2AllProbes-method | Class "DatPkg" |
| KEGGHyperGParams-class | Class "KEGGHyperGParams" and "PFAMHyperGParams" |
| KEGGHyperGResult-class | Class "HyperGResult" |
-- L --
| level2nodes | Class "ChrBandTree" |
| level2nodes-method | Class "ChrBandTree" |
| lgeneIds | Class "ChrBandTree" |
| lgeneIds-method | Class "ChrBandTree" |
| LinearMParams-class | Class "LinearMParams" |
| LinearMResult-class | Class "LinearMResult" |
| LinearMResultBase-class | Class "LinearMResultBase" |
| linearMTest | A linear model-based test to detect enrichment of unusual genes in categories |
| linearMTest-method | A linear model-based test to detect enrichment of unusual genes in categories |
-- M --
| makeChrBandGraph | Create a graph representing chromosome band annotation data |
| makeChrBandGSC | Mapping chromosome bands to genes |
| makeChrBandInciMat | Mapping chromosome bands to genes |
| makeEBcontr | A function to make the contrast vectors needed for EBarrays |
| makeValidParams | Non-standard Generic for Checking Validity of Parameter Objects |
| makeValidParams-method | Class "HyperGParams" |
| MAPAmat | Mapping chromosome bands to genes |
-- N --
| NewChrBandTree | Create a new ChrBandTree object |
-- O --
| OBOCollectionDatPkg | Class "DatPkg" |
| OBOCollectionDatPkg-class | Class "DatPkg" |
| OBOHyperGParams | Class "OBOHyperGParams" |
| OBOHyperGParams-class | Class "OBOHyperGParams" |
| oddsRatios | Accessors for HyperGResult Objects |
| oddsRatios-method | Accessors for HyperGResult Objects |
| ontology | Class "HyperGParams" |
| ontology-method | Class "GOHyperGParams" |
| ontology-method | Class "HyperGParams" |
| ontology<- | Class "HyperGParams" |
| ontology<--method | Class "GOHyperGParams" |
| Org.XX.egDatPkg-class | Class "DatPkg" |
| organism-method | Class "DatPkg" |
| organism-method | Class "HyperGParams" |
| organism-method | Accessors for HyperGResult Objects |
-- P --
| parentOf | Class "ChrBandTree" |
| parentOf-method | Class "ChrBandTree" |
| PFAMHyperGParams-class | Class "KEGGHyperGParams" and "PFAMHyperGParams" |
| PFAMHyperGResult-class | Class "HyperGResult" |
| probes2MAP | Map probe IDs to MAP regions. |
| probes2Path | A function to map probe identifiers to pathways. |
| pvalueCutoff | Accessors for HyperGResult Objects |
| pvalueCutoff-method | Class "HyperGParams" |
| pvalueCutoff-method | Accessors for HyperGResult Objects |
| pvalueCutoff-method | Class "LinearMParams" |
| pvalueCutoff-method | Class "LinearMResultBase" |
| pvalueCutoff<- | Class "HyperGParams" |
| pvalueCutoff<--method | Class "HyperGParams" |
| pvalueCutoff<--method | Class "LinearMParams" |
| pvalues | Accessors for HyperGResult Objects |
| pvalues-method | Accessors for HyperGResult Objects |
| pvalues-method | Class "LinearMResult" |
-- S --
| show-method | Class "ChrBandTree" |
| show-method | Class "GOHyperGParams" |
| show-method | Class "HyperGParams" |
| show-method | Class "HyperGResultBase" |
| show-method | Class "LinearMParams" |
| show-method | Class "LinearMResultBase" |
| show-method | Class "OBOHyperGParams" |
| sigCategories | Accessors for HyperGResult Objects |
| sigCategories-method | Accessors for HyperGResult Objects |
| sigCategories-method | Class "LinearMResultBase" |
| summary-method | Accessors for HyperGResult Objects |
| summary-method | Class "LinearMResult" |
| summary-method | Class "LinearMResultBase" |
-- T --
| testDirection | Accessors for HyperGResult Objects |
| testDirection-method | Class "HyperGParams" |
| testDirection-method | Accessors for HyperGResult Objects |
| testDirection-method | Class "LinearMParams" |
| testDirection-method | Class "LinearMResultBase" |
| testDirection<- | Class "HyperGParams" |
| testDirection<--method | Class "HyperGParams" |
| testDirection<--method | Class "LinearMParams" |
| testName | Accessors for HyperGResult Objects |
| testName-method | Accessors for HyperGResult Objects |
| testName-method | Class "LinearMResultBase" |
| treeLevels | Class "ChrBandTree" |
| treeLevels-method | Class "ChrBandTree" |
| ttperm | A simple function to compute a permutation t-test. |
-- U --
| universeBuilder | Return a vector of gene identifiers with category annotations |
| universeBuilder-method | Return a vector of gene identifiers with category annotations |
| universeCounts | Accessors for HyperGResult Objects |
| universeCounts-method | Accessors for HyperGResult Objects |
| universeCounts-method | Class "LinearMResultBase" |
| universeGeneIds | Class "HyperGParams" |
| universeGeneIds-method | Class "HyperGParams" |
| universeGeneIds-method | Class "LinearMParams" |
| universeMappedCount | Accessors for HyperGResult Objects |
| universeMappedCount-method | Accessors for HyperGResult Objects |
| universeMappedCount-method | Class "LinearMResultBase" |
-- Y --
| YeastDatPkg-class | Class "DatPkg" |