Category v2.38.0

Category Analysis

A collection of tools for performing category analysis.

Functions in Category

Name Description
HyperGResultBase-class Class "HyperGResultBase"
cb_contingency Create and Test Contingency Tables of Chromosome Band Annotations
cb_parse_band_Hs Parse Homo Sapiens Chromosome Band Annotations
hyperGTest Hypergeometric Test for association of categories and genes
probes2Path A function to map probe identifiers to pathways.
getPathNames A function to print pathway names given their numeric ID.
MAPAmat Mapping chromosome bands to genes
cateGOry Construct a category membership matrix from a list of gene identifiers and their annotated GO categories.
applyByCategory Apply a function to a vector of statistics, by category
LinearMResult-class Class "LinearMResult"
universeBuilder Return a vector of gene identifiers with category annotations
categoryToEntrezBuilder Return a list mapping category ids to Entrez Gene ids
findAMstats Compute per category summary statistics
makeEBcontr A function to make the contrast vectors needed for EBarrays
cb_test Chromosome Band Tree-Based Hypothesis Testing
gseattperm Permutation p-values for GSEA
linearMTest A linear model-based test to detect enrichment of unusual genes in categories
ChrBandTree-class Class "ChrBandTree"
LinearMParams-class Class "LinearMParams"
hyperg Hypergeometric (gene set enrichment) tests on character vectors.
probes2MAP Map probe IDs to MAP regions.
DatPkg-class Class "DatPkg"
cb_parse_band_Mm Parse Mus Musculus Chromosome Band Annotations
ChrMapHyperGResult-class Class "ChrMapHyperGResult"
local_test_factory Local and Global Test Function Factories
ChrMapHyperGParams-class Class "ChrMapHyperGParams"
HyperGParams-class Class "HyperGParams"
ChrMapLinearMParams-class Class "ChrMapLinearMParams"
exampleLevels Display a sample node from each level of a ChrBandTree object
tree_visitor Tree Visitor Function
ChrMapLinearMResult-class Class "ChrMapLinearMResult"
GSEAGOHyperGParams Helper function for constructing a GOHyperGParams objects or KEGGHyperGParams objects from a GeneSetCollection
HyperGResult-accessors Accessors for HyperGResult Objects
Category-defunct Defunct Functions in Package Category
KEGGHyperGParams-class Class "KEGGHyperGParams" and "PFAMHyperGParams"
GOHyperGParams-class Class "GOHyperGParams"
NewChrBandTree Create a new ChrBandTree object
makeValidParams Non-standard Generic for Checking Validity of Parameter Objects
ttperm A simple function to compute a permutation t-test.
LinearMResultBase-class Class "LinearMResultBase"
effectSize Extract estimated effect sizes
HyperGResult-class Class "HyperGResult"
makeChrBandGraph Create a graph representing chromosome band annotation data
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Details

License Artistic-2.0
LazyLoad Yes
Collate AllClasses.R AllGenerics.R categoryToEntrezBuilder-methods.R categoryName-methods.R hyperg-methods.R hyperGTest-methods.R linearMTest-methods.R DatPkg-accessors.R ChrBandTree.R tree_visitor.R cb_test.R initialize-methods.R HyperGParams-accessors.R LinearMParams-accessors.R HyperGResult-accessors.R LinearMResult-accessors.R ChrMapHyperGResult-accessors.R ChrMapLinearMResult-accessors.R show-methods.R universeBuilder-methods.R utils.R MAPcode.R catcode.R cateGOryMatrix.R gseaperm.R summary-methods.R mouse.R
biocViews Annotation, GO, Pathways, GeneSetEnrichment

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