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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("mgsa")
AuthorSebastian Bauer <mail@sebastianbauer.info>, Julien Gagneur <gagneur@genzentrum.lmu.de>
Bioconductor views GO GeneSetEnrichment Pathways
Date of publicationNone
MaintainerSebastian Bauer <mail@sebastianbauer.info>
LicenseArtistic-2.0
Version1.24.0
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

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

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

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

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