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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
1.32.0
1.30.0
1.28.0
1.26.0
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Version
1.32.0
License
GPL-2
Maintainer
Alex Lewin
Last Published
January 1st, 1970
Functions in BGmix (1.32.0)
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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