Bayesian models for differential gene expression


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Documentation for package ‘BGmix’ version 1.2.0

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BGmix-package BGmix fits a variety of Bayesian hierarchical models for finding differential gene expression between 2 or more experimental conditions.
BGmix Fit the BGmix differential expression model.
calcFDR Estimate the FDR (false discovery rate) and related quantities for BGmix output.
ccParams Read posterior means and classification probabilities from BGmix
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