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 |