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mgsa (version 1.16.0)

Model-based gene set analysis

Description

Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.

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Version

Version

1.16.0

License

Artistic-2.0

Issues

1

Pull Requests

2

Stars

5

Forks

5

Maintainer

Sebastian Bauer

Last Published

February 15th, 2017

Functions in mgsa (1.16.0)

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
mgsa

Performs an MGSA analysis
mgsa-package

Model-based gene set analysis
setsMcmcPost

posterior estimates of the the set marginal probabilities for each MCMC run
setsResults

Posterior for each set
betaMcmcPost

posterior estimates of the parameter beta for each MCMC run
pMcmcPost

posterior estimates of the parameter p for each MCMC run
betaPost

Posterior for beta
populationSize

Size of the population of a MgsaResults
MgsaResults

Results of an MGSA analysis
MgsaSets

Sets of items and their annotations
restarts

How many MCMC runs
example-o

Example objects for mgsa
steps

How many steps per MCMC run
itemAnnotations

Item annotations of a MgsaSets
studySetSizeInPopulation

Size of the study set of a MgsaResults
setAnnotations

Set annotations of a MgsaSets
length,MgsaSets-method

Length of a MgsaSets.
itemIndices

Item indices of a MgsaSets
nsamples

How many samples per MCMC run collected
plot,MgsaResults-method

Plot method for MgsaResults objects
subMgsaSets

Subset of an MgsaSets
pPost

Posterior for beta
readGAF

Read a Gene Ontology annotation file
alphaMcmcPost

posterior estimates of the parameter alpha for each MCMC run
alphaPost

Posterior for alpha
MgsaGoSets

Gene Ontology annotations
show,MgsaResults-method

Show an MgsaResults
MgsaMcmcResults

Instances of this class are used to hold the additional information that was provided by running (possibly multiple times) an MCMC algorithm.
show,MgsaSets-method

Show an MgsaSets