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 |