Category: Category Analysis

A collection of tools for performing category analysis.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Category")
AuthorR. Gentleman with contributions from S. Falcon and D.Sarkar
Bioconductor views Annotation GO GeneSetEnrichment Pathways
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version2.42.0

View on Bioconductor

Man pages

applyByCategory: Apply a function to a vector of statistics, by category

Category-defunct: Defunct Functions in Package 'Category'

cateGOryMatrix: Construct a category membership matrix from a list of gene...

categoryToEntrezBuilder: Return a list mapping category ids to Entrez Gene ids

cb_contingency: Create and Test Contingency Tables of Chromosome Band...

cb_parse_band_Hs: Parse Homo Sapiens Chromosome Band Annotations

cb_parse_band_Mm: Parse Mus Musculus Chromosome Band Annotations

cb_test: Chromosome Band Tree-Based Hypothesis Testing

ChrBandTree-class: Class "ChrBandTree"

ChrMapHyperGParams-class: Class "ChrMapHyperGParams"

ChrMapHyperGResult-class: Class "ChrMapHyperGResult"

ChrMapLinearMParams-class: Class "ChrMapLinearMParams"

ChrMapLinearMResult-class: Class "ChrMapLinearMResult"

DatPkg-class: Class "DatPkg"

effectSize: Extract estimated effect sizes

exampleLevels: Display a sample node from each level of a ChrBandTree object

findAMstats: Compute per category summary statistics

getPathNames: A function to print pathway names given their numeric ID.

GOHyperGParams-class: Class "GOHyperGParams"

GSEAGOHyperGParams: Helper function for constructing a GOHyperGParams objects or...

gseattperm: Permutation p-values for GSEA

hyperg: Hypergeometric (gene set enrichment) tests on character...

HyperGParams-class: Class "HyperGParams"

HyperGResult-accessors: Accessors for HyperGResult Objects

HyperGResultBase-class: Class "HyperGResultBase"

HyperGResult-class: Class "HyperGResult"

hyperGTest: Hypergeometric Test for association of categories and genes

KEGGHyperGParams-class: Class "KEGGHyperGParams" and "PFAMHyperGParams"

LinearMParams-class: Class "LinearMParams"

LinearMResultBase-class: Class "LinearMResultBase"

LinearMResult-class: Class "LinearMResult"

linearMTest: A linear model-based test to detect enrichment of unusual...

local_test_factory: Local and Global Test Function Factories

makeChrBandGraph: Create a graph representing chromosome band annotation data

makeEBcontr: A function to make the contrast vectors needed for EBarrays

makeValidParams: Non-standard Generic for Checking Validity of Parameter...

MAPAmat: Mapping chromosome bands to genes

NewChrBandTree: Create a new ChrBandTree object

probes2MAP: Map probe IDs to MAP regions.

probes2Path: A function to map probe identifiers to pathways.

tree_visitor: Tree Visitor Function

ttperm: A simple function to compute a permutation t-test.

universeBuilder: Return a vector of gene identifiers with category annotations

Functions

. Man page
AffyDatPkg-class Man page
allGeneIds Man page
allGeneIds,ChrBandTree-method Man page
annotation Man page
annotation,GOHyperGParams-method Man page
annotation<-,HyperGParams,character-method Man page
annotation,HyperGParams-method Man page
annotation,HyperGResultBase-method Man page
annotation<-,LinearMParams,character-method Man page
annotation,LinearMParams-method Man page
annotation,LinearMResultBase-method Man page
applyByCategory Man page
bottomup_tree_visitor Man page
cateGOry Man page
Category-defunct Man page
categoryName Man page
categoryName,GOHyperGParams-method Man page
categoryName,HyperGParams-method Man page
categoryName,LinearMParams-method Man page
categoryToEntrezBuilder Man page
categoryToEntrezBuilder,GOHyperGParams-method Man page
categoryToEntrezBuilder,KEGGHyperGParams-method Man page
categoryToEntrezBuilder,PFAMHyperGParams-method Man page
cb_children Man page
cb_contingency Man page
cb_parse_band_Hs Man page
cb_parse_band_hsa Man page
cb_parse_band_Mm Man page
cb_sigBands Man page
cb_test Man page
childrenOf Man page
childrenOf,ChrBandTree,character-method Man page
chrBandInciMat Man page
ChrBandTree-class Man page
ChrBandTreeFromGraph Man page
chrGraph Man page
chrGraph,ChrMapHyperGResult-method Man page
chrGraph,ChrMapLinearMResult-method Man page
ChrMapHyperGParams-class Man page
ChrMapHyperGResult-class Man page
ChrMapLinearMParams-class Man page
ChrMapLinearMResult-class Man page
condGeneIdUniverse Man page
conditional Man page
conditional<- Man page
conditional<-,ChrMapHyperGParams,logical-method Man page
conditional,ChrMapHyperGParams-method Man page
conditional,ChrMapHyperGResult-method Man page
conditional<-,GOHyperGParams,logical-method Man page
conditional,GOHyperGParams-method Man page
conditional,HyperGParams-method Man page
conditional,HyperGResultBase-method Man page
conditional<-,LinearMParams,logical-method Man page
conditional,LinearMParams-method Man page
conditional,LinearMResultBase-method Man page
DatPkg-class Man page
DatPkgFactory Man page
DatPkgFactory,character-method Man page
description Man page
description,HyperGResultBase-method Man page
description,LinearMResultBase-method Man page
effectSize Man page
effectSize,LinearMResult-method Man page
exampleLevels Man page
expectedCounts Man page
expectedCounts,ChrMapHyperGResult-method Man page
expectedCounts,HyperGResult-method Man page
findAMstats Man page
geneCounts Man page
geneCounts,HyperGResultBase-method Man page
geneGoHyperGeoTest Man page
geneIds Man page
geneIds<- Man page
geneIdsByCategory Man page
geneIdsByCategory,HyperGResultBase-method Man page
geneIdsByCategory,LinearMResultBase-method Man page
geneIds,ChrBandTree-method Man page
geneIds<-,HyperGParams,ANY-method Man page
geneIds<-,HyperGParams,logical-method Man page
geneIds,HyperGParams-method Man page
geneIds,HyperGResultBase-method Man page
geneIds<-,LinearMParams,ANY-method Man page
geneIds,LinearMParams-method Man page
geneIds,LinearMResultBase-method Man page
geneIdUniverse Man page
geneIdUniverse,ChrMapHyperGResult-method Man page
geneIdUniverse,HyperGResult-method Man page
geneIdUniverse,LinearMResultBase-method Man page
geneKeggHyperGeoTest Man page
geneMappedCount Man page
geneMappedCount Man page
geneMappedCount,HyperGResultBase-method Man page
geneMappedCount,LinearMResultBase-method Man page
GeneSetCollectionDatPkg Man page
getPathNames Man page
GO2AllProbes Man page
GO2AllProbes,DatPkg-method Man page
GO2AllProbes,GeneSetCollectionDatPkg-method Man page
GO2AllProbes,Org.XX.egDatPkg-method Man page
GO2AllProbes,YeastDatPkg-method Man page
GOHyperGParams-class Man page
GSEAGOHyperGParams Man page
GSEAKEGGHyperGParams Man page
gseattperm Man page
hg_test_factory Man page
htmlReport Man page
htmlReport,HyperGResultBase-method Man page
htmlReport,KEGGHyperGResult-method Man page
htmlReport,PFAMHyperGResult-method Man page
hyperg Man page
hyperg,character-method Man page
hyperg,list-method Man page
HyperGParams-class Man page
HyperGResult-accessors Man page
HyperGResultBase-class Man page
HyperGResult-class Man page
hyperGTest Man page
hyperGTest,ChrMapHyperGParams-method Man page
hyperGTest,HyperGParams-method Man page
hyperGTest,KEGGHyperGParams-method Man page
hyperGTest,PFAMHyperGParams-method Man page
ID2EntrezID Man page
ID2EntrezID,AffyDatPkg-method Man page
ID2EntrezID,ArabidopsisDatPkg-method Man page
ID2EntrezID,GeneSetCollectionDatPkg-method Man page
ID2EntrezID,Org.XX.egDatPkg-method Man page
ID2EntrezID,YeastDatPkg-method Man page
ID2GO Man page
ID2GO,DatPkg-method Man page
ID2GO,GeneSetCollectionDatPkg-method Man page
ID2KEGG Man page
ID2KEGG,DatPkg-method Man page
ID2KEGG,GeneSetCollectionDatPkg-method Man page
initialize,HyperGParams-method Man page
isConditional Man page
isDBDatPkg,DatPkg-method Man page
isDBDatPkg,GeneSetCollectionDatPkg-method Man page
KEGG2AllProbes Man page
KEGG2AllProbes,DatPkg-method Man page
KEGG2AllProbes,GeneSetCollectionDatPkg-method Man page
KEGGHyperGParams-class Man page
KEGGHyperGResult-class Man page
level2nodes Man page
level2nodes,ChrBandTree,character-method Man page
level2nodes,ChrBandTree,numeric-method Man page
lgeneIds Man page
lgeneIds,ChrBandTree-method Man page
LinearMParams-class Man page
LinearMResultBase-class Man page
LinearMResult-class Man page
linearMTest Man page
linearMTest,ChrMapLinearMParams-method Man page
linearMTest,LinearMParams-method Man page
local_test_factory Man page
makeChrBandGraph Man page
makeChrBandGSC Man page
makeChrBandInciMat Man page
makeEBcontr Man page
makeValidParams Man page
makeValidParams,HyperGParams-method Man page
MAPAmat Man page
NewChrBandTree Man page
oddsRatios Man page
oddsRatios,ChrMapHyperGResult-method Man page
oddsRatios,HyperGResult-method Man page
ontology Man page
ontology<- Man page
ontology<-,GOHyperGParams,character-method Man page
ontology,GOHyperGParams-method Man page
ontology,HyperGParams-method Man page
organism,DatPkg-method Man page
organism,GeneSetCollectionDatPkg-method Man page
organism,HyperGParams-method Man page
organism,HyperGResult-method Man page
Org.XX.egDatPkg-class Man page
parentOf Man page
parentOf,ChrBandTree,character-method Man page
PFAMHyperGParams-class Man page
PFAMHyperGResult-class Man page
probes2MAP Man page
probes2Path Man page
pvalueCutoff Man page
pvalueCutoff<- Man page
pvalueCutoff<-,HyperGParams-method Man page
pvalueCutoff,HyperGParams-method Man page
pvalueCutoff,HyperGResultBase-method Man page
pvalueCutoff<-,LinearMParams-method Man page
pvalueCutoff,LinearMParams-method Man page
pvalueCutoff,LinearMResultBase-method Man page
pvalues Man page
pvalues,ChrMapHyperGResult-method Man page
pvalues,HyperGResult-method Man page
pvalues,LinearMResult-method Man page
show,ChrBandTree-method Man page
show,GOHyperGParams-method Man page
show,HyperGParams-method Man page
show,HyperGResultBase-method Man page
show,LinearMParams-method Man page
show,LinearMResultBase-method Man page
sigCategories Man page
sigCategories,HyperGResultBase-method Man page
sigCategories,LinearMResultBase-method Man page
summary,HyperGResultBase-method Man page
summary,KEGGHyperGResult-method Man page
summary,LinearMResultBase-method Man page
summary,LinearMResult-method Man page
summary,PFAMHyperGResult-method Man page
testDirection Man page
testDirection<- Man page
testDirection<-,HyperGParams-method Man page
testDirection,HyperGParams-method Man page
testDirection,HyperGResultBase-method Man page
testDirection<-,LinearMParams-method Man page
testDirection,LinearMParams-method Man page
testDirection,LinearMResultBase-method Man page
testName Man page
testName,HyperGResultBase-method Man page
testName,LinearMResultBase-method Man page
topdown_tree_visitor Man page
treeLevels Man page
treeLevels,ChrBandTree-method Man page
tree_visitor Man page
ttperm Man page
universeBuilder Man page
universeBuilder,GOHyperGParams-method Man page
universeBuilder,KEGGHyperGParams-method Man page
universeBuilder,PFAMHyperGParams-method Man page
universeCounts Man page
universeCounts,HyperGResultBase-method Man page
universeCounts,LinearMResultBase-method Man page
universeGeneIds Man page
universeGeneIds,HyperGParams-method Man page
universeGeneIds,LinearMParams-method Man page
universeMappedCount Man page
universeMappedCount,HyperGResultBase-method Man page
universeMappedCount,LinearMResultBase-method Man page
YeastDatPkg-class Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllGenerics.R R/ChrBandTree.R R/ChrMapHyperGResult-accessors.R R/ChrMapLinearMResult-accessors.R R/DatPkg-accessors.R R/HyperGParams-accessors.R R/HyperGResult-accessors.R R/LinearMParams-accessors.R R/LinearMResult-accessors.R R/MAPcode.R R/catcode.R R/cateGOryMatrix.R R/categoryName-methods.R R/categoryToEntrezBuilder-methods.R R/cb_test.R R/gseaperm.R R/hyperGTest-methods.R R/hyperg-methods.R R/initialize-methods.R R/linearMTest-methods.R R/mouse.R R/show-methods.R R/summary-methods.R R/tree_visitor.R R/universeBuilder-methods.R R/utils.R
TODO
build
build/vignette.rds
inst
inst/NEWS
inst/UnitTests
inst/UnitTests/HyperGParams_test.R
inst/UnitTests/Makefile_tests
inst/UnitTests/ghgans10.rda
inst/UnitTests/hyperGTest_KEGG_test.R inst/UnitTests/hyperGTest_PFAM_test.R inst/UnitTests/hyperGTest_test.R
inst/UnitTests/runall.sh
inst/UnitTests/runalltests.R
inst/UnitTests/runfile.sh
inst/doc
inst/doc/Category.R
inst/doc/Category.Rnw
inst/doc/Category.pdf
inst/doc/ChromBand.R
inst/doc/ChromBand.Rnw
inst/doc/ChromBand.pdf
inst/scripts
inst/scripts/CLLex.R
man
man/Category-defunct.Rd man/ChrBandTree-class.Rd man/ChrMapHyperGParams-class.Rd man/ChrMapHyperGResult-class.Rd man/ChrMapLinearMParams-class.Rd man/ChrMapLinearMResult-class.Rd man/DatPkg-class.Rd man/GOHyperGParams-class.Rd man/GSEAGOHyperGParams.Rd man/HyperGParams-class.Rd man/HyperGResult-accessors.Rd man/HyperGResult-class.Rd man/HyperGResultBase-class.Rd man/KEGGHyperGParams-class.Rd man/LinearMParams-class.Rd man/LinearMResult-class.Rd man/LinearMResultBase-class.Rd man/MAPAmat.Rd man/NewChrBandTree.Rd man/applyByCategory.Rd man/cateGOryMatrix.Rd man/categoryToEntrezBuilder.Rd man/cb_contingency.Rd man/cb_parse_band_Hs.Rd man/cb_parse_band_Mm.Rd man/cb_test.Rd man/effectSize.Rd man/exampleLevels.Rd man/findAMstats.Rd man/getPathNames.Rd man/gseattperm.Rd man/hyperGTest.Rd man/hyperg.Rd man/linearMTest.Rd man/local_test_factory.Rd man/makeChrBandGraph.Rd man/makeEBcontr.Rd man/makeValidParams.Rd man/probes2MAP.Rd man/probes2Path.Rd man/tree_visitor.Rd man/ttperm.Rd man/universeBuilder.Rd
tests
tests/runTests.R
vignettes
vignettes/Category.Rnw
vignettes/ChromBand.Rnw
vignettes/cat.bib

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