mgsa: Model-based gene set analysis

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.

Author
Sebastian Bauer <mail@sebastianbauer.info>, Julien Gagneur <gagneur@genzentrum.lmu.de>
Date of publication
None
Maintainer
Sebastian Bauer <mail@sebastianbauer.info>
License
Artistic-2.0
Version
1.22.0
URLs

View on Bioconductor

Man pages

alphaMcmcPost-methods
posterior estimates of the parameter alpha for each MCMC run
alphaPost-methods
Posterior for alpha
betaMcmcPost-methods
posterior estimates of the parameter beta for each MCMC run
betaPost-methods
Posterior for beta
createMgsaGoSets
This functions takes a 1:1 mapping of go.ids to items and...
example-go
Example GO sets for mgsa
example-o
Example objects for mgsa
itemAnnotations-methods
Item annotations of a MgsaSets
itemIndices-methods
Item indices of a MgsaSets
length-methods
Length of a MgsaSets.
MgsaGoSets-class
Gene Ontology annotations
MgsaMcmcResults-class
Instances of this class are used to hold the additional...
mgsa-methods
Performs an MGSA analysis
mgsa-package
Model-based gene set analysis
MgsaResults-class
Results of an MGSA analysis
MgsaSets-class
Sets of items and their annotations
nsamples-methods
How many samples per MCMC run collected
plot-MgsaResults-method
Plot method for MgsaResults objects
pMcmcPost-methods
posterior estimates of the parameter p for each MCMC run
populationSize-methods
Size of the population of a MgsaResults
pPost-methods
Posterior for beta
readGAF
Read a Gene Ontology annotation file
restarts-methods
How many MCMC runs
setAnnotations-methods
Set annotations of a MgsaSets
setsMcmcPost-methods
posterior estimates of the the set marginal probabilities for...
setsResults-methods
Posterior for each set
show-MgsaResults-method
Show an MgsaResults
show-MgsaSets-method
Show an MgsaSets
steps-methods
How many steps per MCMC run
studySetSizeInPopulation-methods
Size of the study set of a MgsaResults
subMgsaSets-methods
Subset of an MgsaSets

Files in this package

mgsa/CHANGES
mgsa/DESCRIPTION
mgsa/NAMESPACE
mgsa/R
mgsa/R/MgsaGoSets-class.R
mgsa/R/MgsaResults-class.R
mgsa/R/MgsaSets-class.R
mgsa/R/dottedTable.R
mgsa/R/mgsa-methods.R
mgsa/R/mgsa-package.R
mgsa/R/zzz.R
mgsa/README.md
mgsa/acinclude.m4
mgsa/aclocal.m4
mgsa/build
mgsa/build/vignette.rds
mgsa/cleanup
mgsa/configure
mgsa/configure.ac
mgsa/data
mgsa/data/example.rda
mgsa/inst
mgsa/inst/doc
mgsa/inst/doc/mgsa.R
mgsa/inst/doc/mgsa.Rnw
mgsa/inst/doc/mgsa.pdf
mgsa/inst/example_files
mgsa/inst/example_files/gene_association_head.sgd
mgsa/man
mgsa/man/MgsaGoSets-class.Rd
mgsa/man/MgsaMcmcResults-class.Rd
mgsa/man/MgsaResults-class.Rd
mgsa/man/MgsaSets-class.Rd
mgsa/man/alphaMcmcPost-methods.Rd
mgsa/man/alphaPost-methods.Rd
mgsa/man/betaMcmcPost-methods.Rd
mgsa/man/betaPost-methods.Rd
mgsa/man/createMgsaGoSets.Rd
mgsa/man/example-go.Rd
mgsa/man/example-o.Rd
mgsa/man/itemAnnotations-methods.Rd
mgsa/man/itemIndices-methods.Rd
mgsa/man/length-methods.Rd
mgsa/man/mgsa-methods.Rd
mgsa/man/mgsa-package.Rd
mgsa/man/nsamples-methods.Rd
mgsa/man/pMcmcPost-methods.Rd
mgsa/man/pPost-methods.Rd
mgsa/man/plot-MgsaResults-method.Rd
mgsa/man/populationSize-methods.Rd
mgsa/man/readGAF.Rd
mgsa/man/restarts-methods.Rd
mgsa/man/setAnnotations-methods.Rd
mgsa/man/setsMcmcPost-methods.Rd
mgsa/man/setsResults-methods.Rd
mgsa/man/show-MgsaResults-method.Rd
mgsa/man/show-MgsaSets-method.Rd
mgsa/man/steps-methods.Rd
mgsa/man/studySetSizeInPopulation-methods.Rd
mgsa/man/subMgsaSets-methods.Rd
mgsa/script
mgsa/script/README
mgsa/script/TODO
mgsa/script/buildman.sh
mgsa/script/demo.R
mgsa/script/test.R
mgsa/script/test2.R
mgsa/script/test_GO.R
mgsa/script/test_signature.R
mgsa/script/vignette_quick_example.R
mgsa/src
mgsa/src/Makevars.in
mgsa/src/mgsa.c
mgsa/src/mt19937p
mgsa/src/mt19937p/example-mt.c
mgsa/src/mt19937p/mt19937p.c
mgsa/src/mt19937p/mt19937p.h
mgsa/tests
mgsa/tests/testthat
mgsa/tests/testthat.R
mgsa/tests/testthat/gene_association_head.goa_ref_human.gz
mgsa/tests/testthat/test-mgsa.R
mgsa/tests/testthat/test-readGAF.R
mgsa/tests/testthat/test-subMgsaSets.R
mgsa/vignettes
mgsa/vignettes/mgsa.Rnw