Model-based gene set analysis


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Documentation for package ‘mgsa’ version 1.6.0

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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
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
createMgsaGoSets This functions takes a 1:1 mapping of go...
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
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