alphaMcmcPost           posterior estimates of the parameter alpha for
                        each MCMC run
alphaPost               Posterior for alpha
betaMcmcPost            posterior estimates of the parameter beta for
                        each MCMC run
betaPost                Posterior for beta
createMgsaGoSets        This functions takes a 1:1 mapping of go.ids to
                        items and returns a full MgsaGOSets instance.
                        The structure of GO is gathered from GO.db. It
                        is sufficient to specify just the directly
                        asserted mapping (or annotation), i.e., the
                        most specific ones. The true path rule is taken
                        account, that is, if an item is annotated to a
                        term then it will be also annotated to more
                        general terms (some people prefer to say that
                        just the transitive closure is calculated).
example-go              Example GO sets for mgsa
example-o               Example objects for mgsa
itemAnnotations         Item annotations of a MgsaSets
itemIndices             Item indices of a MgsaSets
length,MgsaSets-method
                        Length of a MgsaSets.
mgsa                    Performs an MGSA analysis
mgsa-package            Model-based gene set analysis
MgsaGoSets-class        Gene Ontology annotations
MgsaMcmcResults-class   Instances of this class are used to hold the
                        additional information that was provided by
                        running (possibly multiple times) an MCMC
                        algorithm.
MgsaResults-class       Results of an MGSA analysis
MgsaSets-class          Sets of items and their annotations
nsamples                How many samples per MCMC run collected
plot,MgsaResults-method
                        Plot method for MgsaResults objects
pMcmcPost               posterior estimates of the parameter p for each
                        MCMC run
populationSize          Size of the population of a MgsaResults
pPost                   Posterior for beta
readGAF                 Read a Gene Ontology annotation file
restarts                How many MCMC runs
setAnnotations          Set annotations of a MgsaSets
setsMcmcPost            posterior estimates of the the set marginal
                        probabilities for each MCMC run
setsResults             Posterior for each set
show,MgsaResults-method
                        Show an MgsaResults
show,MgsaSets-method    Show an MgsaSets
steps                   How many steps per MCMC run
studySetSizeInPopulation
                        Size of the study set of a MgsaResults
subMgsaSets             Subset of an MgsaSets
