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.

AuthorSebastian Bauer <mail@sebastianbauer.info>, Julien Gagneur <gagneur@genzentrum.lmu.de>
Date of publicationNone
MaintainerSebastian Bauer <mail@sebastianbauer.info>
LicenseArtistic-2.0
Version1.22.0
https://github.com/sba1/mgsa-bioc

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

Functions

alphaMcmcPost Man page
alphaMcmcPost,MgsaMcmcResults-method Man page
alphaPost Man page
alphaPost,MgsaResults-method Man page
betaMcmcPost Man page
betaMcmcPost,MgsaMcmcResults-method Man page
betaPost Man page
betaPost,MgsaResults-method Man page
createMgsaGoSets Man page
example_go Man page
example-go Man page
example_o Man page
example-o Man page
itemAnnotations Man page
itemAnnotations,MgsaSets,character-method Man page
itemAnnotations,MgsaSets,missing-method Man page
itemIndices Man page
itemIndices,MgsaSets,character-method Man page
itemIndices,MgsaSets,numeric-method Man page
length,MgsaSets-method Man page
mgsa Man page
mgsa,character,list-method Man page
mgsa,character,MgsaSets-method Man page
MgsaGoSets-class Man page
mgsa,integer,list-method Man page
mgsa,logical,list-method Man page
MgsaMcmcResults-class Man page
mgsa,numeric,list-method Man page
mgsa-package Man page
MgsaResults-class Man page
MgsaSets-class Man page
nsamples Man page
nsamples,MgsaMcmcResults-method Man page
plot,MgsaResults-method Man page
pMcmcPost Man page
pMcmcPost,MgsaMcmcResults-method Man page
populationSize Man page
populationSize,MgsaResults-method Man page
pPost Man page
pPost,MgsaResults-method Man page
readGAF Man page
restarts Man page
restarts,MgsaMcmcResults-method Man page
setAnnotations Man page
setAnnotations,MgsaSets,character-method Man page
setAnnotations,MgsaSets,missing-method Man page
setsMcmcPost Man page
setsMcmcPost,MgsaMcmcResults-method Man page
setsResults Man page
setsResults,MgsaResults-method Man page
show,MgsaResults-method Man page
show,MgsaSets-method Man page
steps Man page
steps,MgsaMcmcResults-method Man page
studySetSizeInPopulation Man page
studySetSizeInPopulation,MgsaResults-method Man page
subMgsaSets Man page
subMgsaSets,MgsaSets,character-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.