BGmix v1.32.0

by Alex Lewin

Bayesian models for differential gene expression

Fully Bayesian mixture models for differential gene expression

Functions in BGmix

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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Details

Type Package
License GPL-2
biocViews Microarray, DifferentialExpression, MultipleComparison

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