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