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Category (version 2.38.0)
Category Analysis
Description
A collection of tools for performing category analysis.
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Version
2.38.0
2.36.0
2.34.2
2.32.0
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Version
2.38.0
License
Artistic-2.0
Maintainer
Bioconductor Package Maintainer
Last Published
January 1st, 1970
Functions in Category (2.38.0)
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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