Category-defunct        Defunct Functions in Package 'Category'
ChrBandTree-class       Class "ChrBandTree"
ChrMapHyperGParams-class
                        Class "ChrMapHyperGParams"
ChrMapHyperGResult-class
                        Class "ChrMapHyperGResult"
ChrMapLinearMParams-class
                        Class "ChrMapLinearMParams"
ChrMapLinearMResult-class
                        Class "ChrMapLinearMResult"
DatPkg-class            Class "DatPkg"
GOHyperGParams-class    Class "GOHyperGParams"
GSEAGOHyperGParams      Helper function for constructing a
                        GOHyperGParams objects or KEGGHyperGParams
                        objects from a GeneSetCollection
HyperGParams-class      Class "HyperGParams"
HyperGResult-accessors
                        Accessors for HyperGResult Objects
HyperGResult-class      Class "HyperGResult"
HyperGResultBase-class
                        Class "HyperGResultBase"
KEGGHyperGParams-class
                        Class "KEGGHyperGParams" and "PFAMHyperGParams"
LinearMParams-class     Class "LinearMParams"
LinearMResult-class     Class "LinearMResult"
LinearMResultBase-class
                        Class "LinearMResultBase"
MAPAmat                 Mapping chromosome bands to genes
NewChrBandTree          Create a new ChrBandTree object
OBOHyperGParams-class   Class "OBOHyperGParams"
applyByCategory         Apply a function to a vector of statistics, by
                        category
cateGOry                Construct a category membership matrix from a
                        list of gene identifiers and their annotated GO
                        categories.
categoryToEntrezBuilder
                        Return a list mapping category ids to Entrez
                        Gene ids
cb_contingency          Create and Test Contingency Tables of
                        Chromosome Band Annotations
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
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.
gseattperm              Permutation p-values for GSEA
hyperGTest              Hypergeometric Test for association of
                        categories and genes
hyperg                  Hypergeometric (gene set enrichment) tests on
                        character vectors.
linearMTest             A linear model-based test to detect enrichment
                        of unusual genes in categories
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 Objects
probes2MAP              Map probe IDs to MAP regions.
probes2Path             A function to map probe identifiers to
                        pathways.
ttperm                  A simple function to compute a permutation
                        t-test.
universeBuilder         Return a vector of gene identifiers with
                        category annotations
