BGmix v1.32.0

by Alex Lewin

Bayesian models for differential gene expression

Fully Bayesian mixture models for differential gene expression

Name	Description
ccSummary	Read summary of BGmix output
ccPred	Read predictive quantities output from BGmix.
BGmix-package	BGmix fits a variety of Bayesian hierarchical models for finding differential gene expression between 2 or more experimental conditions.
ccTrace	Read trace files from BGmix
ccParams	Read posterior means and classification probabilities from BGmix
FDRplotTailPP	Plot of FDR for tail posterior probability
EstimatePi0	Proportion of the variables under the null hypothesis
FDRforTailPP	FDR for tail posterior probability
calcFDR	Estimate the FDR (false discovery rate) and related quantities for BGmix output.
BGmix	Fit the BGmix differential expression model.
histTailPP	Histogram plot for tail posterior probability
plotCompare	Scatter plot with equal axes.
Simulated gene expression data	Sample variance of log gene expression under two conditions
plotBasic	Basic plots of BGmix parameters and data.
plotMixDensity	Plot predictive density of data.
plotTrace	Trace plots for BGmix output.
plotPredChecks	Plots of predictive checks for mixture prior.
TailPP	Tail posterior probability for BGmix output.
plotFDR	Plot estimated FDR etc. for BGmix output.
readBGX	Reads output from BGX package, for input to BGmix.
Simulated example data	Mean log gene expression under two conditions
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Type	Package
License	GPL-2
biocViews	Microarray, DifferentialExpression, MultipleComparison

depends	base (>= 2.3.1) , KernSmooth , R (>= 2.3.1)
Contributors	Natalia Bochkina, Alex Lewin