MgsaGoSets-class        Gene Ontology annotations
MgsaMcmcResults-class   MgsaMcmcResults-class
MgsaResults-class       Results of an MGSA analysis
MgsaSets-class          Sets of items and their annotations
alphaMcmcPost-methods   posterior estimates of the parameter alpha for
                        each MCMC run
alphaPost-methods       Posterior for alpha
betaMcmcPost-methods    posterior estimates of the parameter beta for
                        each MCMC run
betaPost-methods        Posterior for beta
example_go              Example GO sets for mgsa
example_o               Example objects for mgsa
itemAnnotations-methods
                        Item annotations of a MgsaSets
itemIndices-methods     Item indices of a MgsaSets
length,MgsaSets-method
                        Length of a MgsaSets.
mgsa-methods            Performs an MGSA analysis
mgsa-package            Model-based gene set analysis
pMcmcPost-methods       posterior estimates of the parameter p for each
                        MCMC run
pPost-methods           Posterior for beta
plot,MgsaResults-method
                        plot,MgsaResults-method
populationSize-methods
                        Size of the population of a MgsaResults
readGAF                 Read a Gene Ontology annotation file
restarts-methods        How many MCMC runs
setAnnotations-methods
                        Set annotations of a MgsaSets
setsMcmcPost-methods    posterior estimates of the the set marginal
                        probabilities for each MCMC run
setsResults-methods     Posterior for each set
show,MgsaResults-method
                        Show an MgsaResults
show,MgsaSets-method    Show an MgsaSets
steps-methods           How many steps per MCMC run
studySetSizeInPopulation-methods
                        Size of the study set of a MgsaResults
subMgsaSets-methods     Subset of an MgsaSets
