R: Model-based gene set analysis

# Model-based gene set analysis

## Documentation for package ‘mgsa’ version 1.61.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

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