CoGAPS: Coordinated Gene Activity in Pattern Sets
Version 2.10.0

Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

AuthorWai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey, Genevieve Stein-O'Brien, Michael Considine, John Stansfield, Shawn Sivy, Carlo Colantuoni, Alexander Favorov, Mike Ochs, Elana Fertig
Bioconductor views Bayesian Clustering DifferentialExpression DimensionReduction GeneExpression GeneSetEnrichment Microarray MultipleComparison RNASeq TimeCourse Transcription
Date of publicationNone
MaintainerElana J. Fertig <ejfertig@jhmi.edu>
LicenseGPL (==2)
Version2.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CoGAPS")

Getting started

Package overview
README.md
GWCoGAPS and PatternMarkers Vignette

Popular man pages

gapsTestRun: 'gapsTestRun' calls the C++ MCMC code and performs Bayesian...
GWCoGAPS: GWCoGAPS
plotAtoms: 'plotAtoms' a simple plot of the number of atoms from one of...
reconstructGene: reconstruct Gene
reOrderBySet: reOrderBySet
residuals: 'residuals' calculate residuals and produce heatmap
SimpSim.A: Simulated data
See all...

All man pages Function index File listing

Man pages

binaryA: 'binaryA' creates a binarized heatmap of the A matrix in...
calcCoGAPSStat: 'calcCoGAPSStat' calculates the gene set statistics for each...
calcGeneGSStat: 'calcGeneGSStat' calculates the probability that a gene...
calcZ: 'calcZ' calculates the Z-score for each element based on...
CoGAPS: 'CoGAPS' calls the C++ MCMC code through gapsRun and performs...
CoGAPS-package: CoGAPS: Coordinated Gene Activity in Pattern Sets
computeGeneGSProb: CoGAPS gene membership statistic
createGWCoGAPSSets: createGWCoGAPSSets
gapsMapRun: 'gapsMapRun' calls the C++ MCMC code and performs Bayesian...
gapsMapTestRun: 'gapsMapTestRun' calls the C++ MCMC code and performs...
gapsRun: 'gapsRun' calls the C++ MCMC code and performs Bayesian...
gapsTestRun: 'gapsTestRun' calls the C++ MCMC code and performs Bayesian...
generateSeeds: generateSeeds
GIST.D: Sample GIST gene expression data from Ochs et al. (2009).
GIST.S: Sample GIST gene expression data from Ochs et al. (2009).
GSets: Simulated dataset to quantify gene set membership.
GWCoGAPS: GWCoGAPS
patternMarkers: patternMarkers
patternMatch4Parallel: patternMatch4Parallel
PatternMatcher: PatternMatcher Shiny Ap
plotAtoms: 'plotAtoms' a simple plot of the number of atoms from one of...
plotDiag: 'plotDiag' plots a series of diagnostic plots
plotGAPS: 'plotGAPS' plots the output A and P matrices as a heatmap and...
plotP: 'plotP' plots the P matrix in a line plot with error bars
plotPatternMarkers: plotPatternMarkers
plotSmoothPatterns: 'plotSmoothPatterns' plots the output A and P matrices as a...
postFixed4Parallel: postFixed4Parallel
reconstructGene: reconstruct Gene
reorderByPatternMatch: 'reorderByPatternMatch' plots the output A and P matrices as...
reOrderBySet: reOrderBySet
residuals: 'residuals' calculate residuals and produce heatmap
SimpSim.A: Simulated data
SimpSim.D: Simulated data
SimpSim.P: Simulated data
SimpSim.S: Simulated data
tf2ugFC: Gene sets defined by transcription factors defined from...

Functions

CoGAPS Man page Source code
CoGAPS-package Man page
GIST.D Man page
GIST.S Man page
GSets Man page Man page
GWCoGAPS Man page Source code
SimpSim.A Man page
SimpSim.D Man page
SimpSim.P Man page
SimpSim.S Man page
binaryA Man page Source code
calcCoGAPSStat Man page Source code
calcGeneGSStat Man page Source code
calcZ Man page Source code
cogaps Source code
cogapsMap Source code
cogapsMapTest Source code
cogapsTest Source code
computeGeneGSProb Man page Source code
createGWCoGAPSSets Man page Source code
gapsInterPattern Source code
gapsIntraPattern Source code
gapsMapRun Man page Source code
gapsMapTestRun Man page Source code
gapsRun Man page Source code
gapsTestRun Man page Source code
geneGSProb Man page
generateSeeds Man page Source code
patternMarkers Man page Source code
patternMatch4Parallel Man page Source code
patternMatcher Man page Source code
plotAtoms Man page Source code
plotDiag Man page Source code
plotGAPS Man page Source code
plotP Man page Source code
plotPatternMarkers Man page Source code
plotSmoothPatterns Man page Source code
postFixed4Parallel Man page Source code
reOrderBySet Man page Source code
reconstructGene Man page Source code
reorderByPatternMatch Man page Source code
residuals Man page Source code
tf2ugFC Man page

Files

COPYING
DESCRIPTION
NAMESPACE
NEWS
R
R/CoGAPS.R
R/GWCoGAPS.R
R/RcppExports.R
R/binaryA.R
R/calcCoGAPSStat.R
R/calcGeneGSStat.R
R/calcZ.R
R/createGWCoGAPSSets.R
R/gapsInterPattern.R
R/gapsIntraPattern.R
R/gapsMapRun.R
R/gapsMapTestRun.R
R/gapsRun.R
R/gapsTestRun.R
R/generateSeeds.R
R/package.R
R/patternMarkers.R
R/patternMatch4Parallel.R
R/patternMatcher.R
R/plotAtoms.R
R/plotDiag.R
R/plotGAPS.R
R/plotP.R
R/plotPatternMarkers.R
R/plotSmoothPatterns.R
R/postFixed4Parallel.R
R/reOrderBySet.R
R/reconstructGene.R
R/reorderByPatternMatch.R
R/residuals.R
README.md
build
build/vignette.rds
data
data/GIST_TS_20084.RData
data/SimpSim.RData
data/TFGSList.RData
inst
inst/CITATION
inst/doc
inst/doc/CoGAPSUsersManual.R
inst/doc/CoGAPSUsersManual.Rnw
inst/doc/CoGAPSUsersManual.pdf
inst/scripts
man
man/CoGAPS-package.Rd
man/CoGAPS.Rd
man/GIST.D.Rd
man/GIST.S.Rd
man/GSets.Rd
man/GWCoGAPS.Rd
man/PatternMatcher.Rd
man/SimpSim.A.Rd
man/SimpSim.D.Rd
man/SimpSim.P.Rd
man/SimpSim.S.Rd
man/binaryA.Rd
man/calcCoGAPSStat.Rd
man/calcGeneGSStat.Rd
man/calcZ.Rd
man/computeGeneGSProb.Rd
man/createGWCoGAPSSets.Rd
man/gapsMapRun.Rd
man/gapsMapTestRun.Rd
man/gapsRun.Rd
man/gapsTestRun.Rd
man/generateSeeds.Rd
man/patternMarkers.Rd
man/patternMatch4Parallel.Rd
man/plotAtoms.Rd
man/plotDiag.Rd
man/plotGAPS.Rd
man/plotP.Rd
man/plotPatternMarkers.Rd
man/plotSmoothPatterns.Rd
man/postFixed4Parallel.Rd
man/reOrderBySet.Rd
man/reconstructGene.Rd
man/reorderByPatternMatch.Rd
man/residuals.Rd
man/tf2ugFC.Rd
src
src/AtomicSupport.cc
src/AtomicSupport.h
src/GAPSNorm.cpp
src/GAPSNorm.h
src/GibbsSampler-atomic.cpp
src/GibbsSampler-init.cpp
src/GibbsSampler-update.cpp
src/GibbsSampler-util.cpp
src/GibbsSampler.h
src/GibbsSamplerMap.cpp
src/GibbsSamplerMap.h
src/Matrix.cpp
src/Matrix.h
src/RcppExports.cpp
src/cogapsR.cpp
src/cogapsmapR.cpp
src/cogapsmaptestR.cpp
src/cogapstestR.cpp
src/randgen.cpp
src/randgen.h
src/sub_func.cpp
src/sub_func.h
tests
tests/testthat
tests/testthat.R
tests/testthat/test_aesthetic.R
tests/testthat/test_gaps.R
tests/testthat/test_seed.R
tests/testthat/test_snaps.R
vignettes
vignettes/AppNote.bib
vignettes/CoGAPSUsersManual.Rnw
vignettes/GISTFigs-Amplitude.pdf
vignettes/GISTFigs-Patterns.pdf
vignettes/GWCoGAPSPMs.pdf
vignettes/GWCoGAPSvignette.Rmd
vignettes/GWCoGAPSvignette.md
vignettes/ManPipePMs.pdf
vignettes/ShinyApp.pdf
vignettes/ShinyApp.tiff
vignettes/chicago.sty
CoGAPS documentation built on May 20, 2017, 9:26 p.m.

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