Category: Category Analysis

A collection of tools for performing category analysis.

AuthorR. Gentleman with contributions from S. Falcon and D.Sarkar
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version2.40.0

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

Files in this package

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

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