BGmix                   Fit the BGmix differential expression model.
BGmix-package           BGmix fits a variety of Bayesian hierarchical
                        models for finding
EstimatePi0             Proportion of the variables under the null
                        hypothesis
FDRforTailPP            FDR for tail posterior probability
FDRplotTailPP           Plot of FDR for tail posterior probability
TailPP                  Tail posterior probability for BGmix output.
calcFDR                 Estimate the FDR (false discovery rate) and
                        related quantities for
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
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
ybar                    Mean log gene expression under two conditions
