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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

Version

2.38.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in Category (2.38.0)

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