Model-based gene set analysis
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Documentation for package ‘mgsa’ version 1.57.0
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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 |
| alphaPost | Posterior for alpha |
| alphaPost-method | 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 |
| betaPost | Posterior for beta |
| betaPost-method | 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 |
| 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 |
| itemIndices | Item indices of a MgsaSets |
| itemIndices-method | Item indices of a MgsaSets |
| length-method | Length of a MgsaSets. |
| mgsa | Performs an MGSA analysis |
| mgsa-method | Performs an MGSA 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 |
| nsamples-method | How many samples per MCMC run collected |
| plot-method | Plot method for MgsaResults objects |
| pMcmcPost | posterior estimates of the parameter p for each MCMC run |
| pMcmcPost-method | 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 |
| pPost | Posterior for beta |
| pPost-method | Posterior for beta |
| readGAF | Read a Gene Ontology annotation file |
| restarts | How many MCMC runs |
| restarts-method | How many MCMC runs |
| setAnnotations | Set annotations of a MgsaSets |
| setAnnotations-method | 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 |
| setsResults | Posterior for each set |
| setsResults-method | 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 |
| studySetSizeInPopulation | Size of the study set of a MgsaResults |
| studySetSizeInPopulation-method | Size of the study set of a MgsaResults |
| subMgsaSets | Subset of an MgsaSets |
| subMgsaSets-method | Subset of an MgsaSets |