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BGmix (version 1.32.0)

Bayesian models for differential gene expression

Description

Fully Bayesian mixture models for differential gene expression

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Version

Version

1.32.0

License

GPL-2

Maintainer

Alex Lewin

Last Published

February 15th, 2017

Functions in BGmix (1.32.0)

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