BGmix: Bayesian models for differential gene expression

Fully Bayesian mixture models for differential gene expression

Author
Alex Lewin, Natalia Bochkina
Date of publication
None
Maintainer
Alex Lewin <a.m.lewin@imperial.ac.uk>
License
GPL-2
Version
1.34.0

View on Bioconductor

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

Files in this package

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