Controlling bias and inflation in association studies using the empirical null distribution

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Documentation for package ‘bacon’ version 1.4.0

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bacon Gibbs sampler
Bacon-class An S4 class container for storing Gibbs Sampler input and output
bias Method to extract the estimated bias from the 'bacon'-object
bias-method Method to extract the estimated bias from the 'bacon'-object
dnormmix density of a k-component normal mixture
es Method to extract inflation- and bias-corrected effect-sizes
es-method Method to extract inflation- and bias-corrected effect-sizes
estimates Method to extract the estimated parameters from the 'bacon'-object
estimates-method Method to extract the estimated parameters from the 'bacon'-object
fit Method to plot mixture fit
fit-method Method to plot mixture fit
inflation Method to extract the estimated inflation from the 'bacon'-object
inflation-method Method to extract the estimated inflation from the 'bacon'-object
meta fixed meta-analysis
meta-method fixed meta-analysis
plot-method plot hist or qq
plotnormmix plot normal mixtures
posteriors Method to plot posterior distribution
posteriors-method Method to plot posterior distribution
pval Method to extract inflation- and bias-corrected P-values
pval-method Method to extract inflation- and bias-corrected P-values
rnormmix sample from a normal mixture
se Method to extract inflation- and bias-corrected standard errors
se-method Method to extract inflation- and bias-corrected standard errors
topTable topTable
topTable-method topTable
traces Method to plot Gibbs sampling traces
traces-method Method to plot Gibbs sampling traces
tstat Method to extract inflation- and bias-corrected test-statistics
tstat-method Method to extract inflation- and bias-corrected test-statistics