Package: mgsa 1.61.0

Sebastian Bauer

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.

Authors:Sebastian Bauer <[email protected]>, Julien Gagneur <[email protected]>

mgsa_1.61.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
mgsa/json (API)

# Install 'mgsa' in R:

install.packages('mgsa', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sba1/mgsa-bioc/issues

Uses libs:

openmp– GCC OpenMP (GOMP) support library

Datasets:

example_go - Example GO sets for mgsa
example_o - Example objects for mgsa

On BioConductor:mgsa-1.61.0(bioc 3.24)mgsa-1.60.0(bioc 3.23)

pathways go genesetenrichment openmp

6.38 score 5 stars 24 scripts 5 mentions 21 exports 5 dependencies

Last updated from:deb59b130f. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	151
linux-devel-arm64	WARNING	153
linux-devel-x86_64	WARNING	196
source / vignettes	OK	192
linux-release-arm64	WARNING	151
linux-release-x86_64	WARNING	215
macos-release-arm64	WARNING	91
macos-release-x86_64	WARNING	195
macos-oldrel-arm64	WARNING	97
macos-oldrel-x86_64	WARNING	209
windows-devel	WARNING	305
windows-release	WARNING	279
windows-oldrel	WARNING	470
wasm-release	OK	113

Exports:alphaMcmcPost alphaPost betaMcmcPost betaPost itemAnnotations itemIndices mgsa nsamples plot pMcmcPost populationSize pPost readGAF restarts setAnnotations setsMcmcPost setsResults show steps studySetSizeInPopulation subMgsaSets

Dependencies:bitops caTools gplots gtools KernSmooth

Overview of the mgsa package.

Rendered frommgsa.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Model-based gene set analysis	mgsa-package
posterior estimates of the parameter alpha for each MCMC run	alphaMcmcPost alphaMcmcPost,MgsaMcmcResults-method
Posterior for alpha	alphaPost alphaPost,MgsaResults-method
posterior estimates of the parameter beta for each MCMC run	betaMcmcPost betaMcmcPost,MgsaMcmcResults-method
Posterior for beta	betaPost betaPost,MgsaResults-method
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).	createMgsaGoSets
Example GO sets for mgsa	example-go example_go
Example objects for mgsa	example-o example_o
Item annotations of a MgsaSets	itemAnnotations itemAnnotations,MgsaSets,character-method itemAnnotations,MgsaSets,missing-method
Item indices of a MgsaSets	itemIndices itemIndices,MgsaSets,character-method itemIndices,MgsaSets,numeric-method
Length of a MgsaSets.	length,MgsaSets-method
Performs an MGSA analysis	mgsa mgsa,character,list-method mgsa,character,MgsaSets-method mgsa,integer,list-method mgsa,logical,list-method mgsa,numeric,list-method
Gene Ontology annotations	MgsaGoSets-class
Instances of this class are used to hold the additional information that was provided by running (possibly multiple times) an MCMC algorithm.	MgsaMcmcResults-class
Results of an MGSA analysis	MgsaResults-class
Sets of items and their annotations	MgsaSets-class
How many samples per MCMC run collected	nsamples nsamples,MgsaMcmcResults-method
Plot method for MgsaResults objects	plot,MgsaResults-method
posterior estimates of the parameter p for each MCMC run	pMcmcPost pMcmcPost,MgsaMcmcResults-method
Size of the population of a MgsaResults	populationSize populationSize,MgsaResults-method
Posterior for beta	pPost pPost,MgsaResults-method
Read a Gene Ontology annotation file	readGAF
How many MCMC runs	restarts restarts,MgsaMcmcResults-method
Set annotations of a MgsaSets	setAnnotations setAnnotations,MgsaSets,character-method setAnnotations,MgsaSets,missing-method
posterior estimates of the the set marginal probabilities for each MCMC run	setsMcmcPost setsMcmcPost,MgsaMcmcResults-method
Posterior for each set	setsResults setsResults,MgsaResults-method
Show an MgsaResults	show,MgsaResults-method
Show an MgsaSets	show,MgsaSets-method
How many steps per MCMC run	steps steps,MgsaMcmcResults-method
Size of the study set of a MgsaResults	studySetSizeInPopulation studySetSizeInPopulation,MgsaResults-method
Subset of an MgsaSets	subMgsaSets subMgsaSets,MgsaSets,character-method