# Category Analysis

## Documentation for package ‘Category’ version 2.56.0

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

## Help Pages

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"