Category: Category Analysis

Share:

A collection of tools for performing category analysis.

Author
R. Gentleman with contributions from S. Falcon and D.Sarkar
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
2.40.0

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