BGmix: Bayesian models for differential gene expression
Version 1.36.0

Fully Bayesian mixture models for differential gene expression

Browse man pages Browse package API and functions Browse package files

AuthorAlex Lewin, Natalia Bochkina
Bioconductor views DifferentialExpression Microarray MultipleComparison
Date of publicationNone
MaintainerAlex Lewin <a.m.lewin@imperial.ac.uk>
LicenseGPL-2
Version1.36.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BGmix")

Man pages

BGmix: Fit the BGmix differential expression model.
BGmix-package: BGmix fits a variety of Bayesian hierarchical models for...
calcFDR: Estimate the FDR (false discovery rate) and related...
ccParams: Read posterior means and classification probabilities from...
ccPred: Read predictive quantities output from BGmix.
ccSummary: Read summary of BGmix output
ccTrace: Read trace files from BGmix
EstimatePi0: Proportion of the variables under the null hypothesis
FDRforTailPP: FDR for tail posterior probability
FDRplotTailPP: Plot of FDR for tail posterior probability
histTailPP: Histogram plot for tail posterior probability
plotBasic: Basic plots of BGmix parameters and data.
plotCompare: Scatter plot with equal axes.
plotFDR: Plot estimated FDR etc. for BGmix output.
plotMixDensity: Plot predictive density of data.
plotPredChecks: Plots of predictive checks for mixture prior.
plotTrace: Trace plots for BGmix output.
readBGX: Reads output from BGX package, for input to BGmix.
ss: Sample variance of log gene expression under two conditions
TailPP: Tail posterior probability for BGmix output.
ybar: Mean log gene expression under two conditions

Functions

BGmix Man page
BGmix-package Man page
EstimatePi0 Man page Source code
FDRforTailPP Man page Source code
FDRplotTailPP Man page Source code
SimulateFromNull Source code
TailPP Man page Source code
TailPPCalculate Source code
calcF0tail Source code
calcFDR Man page
ccParams Man page
ccPred Man page
ccSummary Man page
ccTrace Man page
histTailPP Man page Source code
plotBasic Man page
plotCompare Man page
plotFDR Man page
plotMixDensity Man page
plotPredChecks Man page
plotTrace Man page
readBGX Man page Source code
ss Man page
summaryTailPP Source code
ybar Man page

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/BGmix.R
R/EstimatePi0.R
R/FDRforTailPP.R
R/FDRplotTailPP.R
R/SimulateFromNull.R
R/TailPP.R
R/TailPPCalculate.R
R/calcF0tail.R
R/calcFDR.R
R/ccParams.R
R/ccPred.R
R/ccSummary.R
R/ccTrace.R
R/fitBGmix.R
R/histTailPP.R
R/plotBasic.R
R/plotCompare.R
R/plotFDR.R
R/plotMixDensity.R
R/plotPredChecks.R
R/plotTrace.R
R/readBGX.R
R/summaryTailPP.R
boostIncl.tar.gz
build
build/vignette.rds
configure
configure.ac
configure.win
data
data/ss.R
data/ybar.R
inst
inst/doc
inst/doc/BGmix.R
inst/doc/BGmix.Rnw
inst/doc/BGmix.pdf
man
man/BGmix-package.Rd
man/BGmix.Rd
man/EstimatePi0.Rd
man/FDRforTailPP.Rd
man/FDRplotTailPP.Rd
man/TailPP.Rd
man/calcFDR.Rd
man/ccParams.Rd
man/ccPred.Rd
man/ccSummary.Rd
man/ccTrace.Rd
man/histTailPP.Rd
man/plotBasic.Rd
man/plotCompare.Rd
man/plotFDR.Rd
man/plotMixDensity.Rd
man/plotPredChecks.Rd
man/plotTrace.Rd
man/readBGX.Rd
man/ss.Rd
man/ybar.Rd
src
src/BGmix_main.cpp
src/BGmix_main.h
src/Makevars
src/Makevars.in
src/Makevars.win
src/rand.hh
src/rundir.cpp
src/rundir.hh
src/updates_BGmix.cpp
src/updates_BGmix.h
vignettes
vignettes/BGmix.Rnw
BGmix documentation built on May 20, 2017, 10:38 p.m.