Entry: BGmix-package
Aliases: BGmix-package
Keywords: models
Description: BGmix fits a variety of Bayesian hierarchical models for finding differential gene expression between 2 or more experimental conditions.
URL: ../../../library/BGmix/html/BGmix-package.html

Entry: BGmix
Aliases: BGmix
Keywords: models
Description: Fit the BGmix differential expression model.
URL: ../../../library/BGmix/html/BGmix.html

Entry: EstimatePi0
Aliases: EstimatePi0
Keywords: htest
Description: Proportion of the variables under the null hypothesis
URL: ../../../library/BGmix/html/EstimatePi0.html

Entry: FDRforTailPP
Aliases: FDRforTailPP
Keywords: htest
Description: FDR for tail posterior probability
URL: ../../../library/BGmix/html/FDRforTailPP.html

Entry: FDRplotTailPP
Aliases: FDRplotTailPP
Keywords: hplot
Description: Plot of FDR for tail posterior probability
URL: ../../../library/BGmix/html/FDRplotTailPP.html

Entry: TailPP
Aliases: TailPP
Keywords: htest
Description: Tail posterior probability for BGmix output.
URL: ../../../library/BGmix/html/TailPP.html

Entry: calcFDR
Aliases: calcFDR
Keywords: htest
Description: Estimate the FDR (false discovery rate) and related quantities for BGmix output.
URL: ../../../library/BGmix/html/calcFDR.html

Entry: ccParams
Aliases: ccParams
Keywords: manip
Description: Read posterior means and classification probabilities from BGmix
URL: ../../../library/BGmix/html/ccParams.html

Entry: ccPred
Aliases: ccPred
Keywords: manip
Description: Read predictive quantities output from BGmix.
URL: ../../../library/BGmix/html/ccPred.html

Entry: ccSummary
Aliases: ccSummary
Keywords: manip
Description: Read summary of BGmix output
URL: ../../../library/BGmix/html/ccSummary.html

Entry: ccTrace
Aliases: ccTrace
Keywords: manip
Description: Read trace files from BGmix
URL: ../../../library/BGmix/html/ccTrace.html

Entry: histTailPP
Aliases: histTailPP
Keywords: hplot
Description: Histogram plot for tail posterior probability
URL: ../../../library/BGmix/html/histTailPP.html

Entry: plotBasic
Aliases: plotBasic
Keywords: hplot
Description: Basic plots of BGmix parameters and data.
URL: ../../../library/BGmix/html/plotBasic.html

Entry: plotCompare
Aliases: plotCompare
Keywords: hplot
Description: Scatter plot with equal axes.
URL: ../../../library/BGmix/html/plotCompare.html

Entry: plotFDR
Aliases: plotFDR
Keywords: hplot
Description: Plot estimated FDR etc. for BGmix output.
URL: ../../../library/BGmix/html/plotFDR.html

Entry: plotMixDensity
Aliases: plotMixDensity
Keywords: hplot
Description: Plot predictive density of data.
URL: ../../../library/BGmix/html/plotMixDensity.html

Entry: plotPredChecks
Aliases: plotPredChecks
Keywords: hplot
Description: Plots of predictive checks for mixture prior.
URL: ../../../library/BGmix/html/plotPredChecks.html

Entry: plotTrace
Aliases: plotTrace
Keywords: hplot
Description: Trace plots for BGmix output.
URL: ../../../library/BGmix/html/plotTrace.html

Entry: readBGX
Aliases: readBGX
Keywords: hplot
Description: Reads output from BGX package, for input to BGmix.
URL: ../../../library/BGmix/html/readBGX.html

Entry: Simulated example data
Aliases: ss
Keywords: datasets
Description: Sample variance of log gene expression under two conditions
URL: ../../../library/BGmix/html/ss.html

Entry: Simulated example data
Aliases: ybar
Keywords: datasets
Description: Mean log gene expression under two conditions
URL: ../../../library/BGmix/html/ybar.html
