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

## Documentation for package ‘bacon’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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