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bacon (version 1.0.4)

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

Description

Bacon can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores.

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Version

Version

1.0.4

License

GPL (>= 2)

Issues

0

Pull Requests

1

Stars

0

Forks

1

Maintainer

Maarten van Iterson

Last Published

February 15th, 2017

Functions in bacon (1.0.4)

estimates

Method to extract the estimated parameters from the 'bacon'-object
meta

fixed meta-analysis
plot,Bacon-method

plot hist or qq
dnormmix

density of a k-component normal mixture
Bacon-class

An S4 class container for storing Gibbs Sampler input and output
bacon

Gibbs sampler
fit

Method to plot mixture fit
bias

Method to extract the estimated bias from the 'bacon'-object
es

Method to extract inflation- and bias-corrected effect-sizes
inflation

Method to extract the estimated inflation from the 'bacon'-object
se

Method to extract inflation- and bias-corrected standard errors
posteriors

Method to plot posterior distribution
plotnormmix

plot normal mixtures
topTable

topTable
rnormmix

sample from a normal mixture
traces

Method to plot Gibbs sampling traces
pval

Method to extract inflation- and bias-corrected P-values
tstat

Method to extract inflation- and bias-corrected test-statistics