BAGS: A Bayesian Approach for Geneset Selection

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R package providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest.

Author
Alejandro Quiroz-Zarate
Date of publication
None
Maintainer
Alejandro Quiroz-Zarate <aquiroz@jimmy.harvard.edu>
License
Artistic-2.0
Version
2.14.0

View on Bioconductor

Man pages

AnnotationMFGO
List containing a collection of gene symbols with their...
BAGS-internal
Internal functions of the BAGS package.
BAGS-package
A Bayesian Approach for Geneset Selection (BAGS).
DataGeneSets
Function that filters the gene sets to work with the desired...
Gibbs2
Function obtains the MCMC chains for the parameters of...
Gibbs3
Function obtains the MCMC chains for the parameters of...
Gibbs4
Function obtains the MCMC chains for the parameters of...
Gibbs5
Function obtains the MCMC chains for the parameters of...
MCMCDataSet
Function that transform the dataset into the required format...
ReadGMT
Function that extracts the gene set definition from a .gmt...

Files in this package

BAGS/DESCRIPTION
BAGS/NAMESPACE
BAGS/R
BAGS/R/DataGeneSets.R
BAGS/R/Gibbs2.R
BAGS/R/Gibbs3.R
BAGS/R/Gibbs4.R
BAGS/R/Gibbs5.R
BAGS/R/GrpMean.R
BAGS/R/MCMCDataSet.R
BAGS/R/ReadGMT.R
BAGS/build
BAGS/build/vignette.rds
BAGS/data
BAGS/data/AnnotationMFGO.rda
BAGS/data/datalist
BAGS/inst
BAGS/inst/NEWS
BAGS/inst/doc
BAGS/inst/doc/BAGS.R
BAGS/inst/doc/BAGS.Rnw
BAGS/inst/doc/BAGS.pdf
BAGS/man
BAGS/man/AnnotationMFGO.Rd
BAGS/man/BAGS-internal.Rd
BAGS/man/BAGS-package.Rd
BAGS/man/DataGeneSets.Rd
BAGS/man/Gibbs2.Rd
BAGS/man/Gibbs3.Rd
BAGS/man/Gibbs4.Rd
BAGS/man/Gibbs5.Rd
BAGS/man/MCMCDataSet.Rd
BAGS/man/ReadGMT.Rd
BAGS/src
BAGS/src/Auxiliares.h
BAGS/src/BAGS.c
BAGS/src/FuncionesFast-Final.h
BAGS/src/OpMat.h
BAGS/src/libMatInv.h
BAGS/src/libmat.h
BAGS/vignettes
BAGS/vignettes/BAGS.Rnw