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

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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.

Author
Maarten van Iterson [aut, cre], Erik van Zwet [ctb]
Date of publication
None
Maintainer
Maarten van Iterson <mviterson@gmail.com>
License
GPL (>= 2)
Version
1.2.0
URLs

View on Bioconductor

Man pages

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

Files in this package

bacon/DESCRIPTION
bacon/NAMESPACE
bacon/NEWS
bacon/R
bacon/R/BaconClass.R
bacon/R/BaconMethods.R
bacon/R/bacon.R
bacon/R/normmixture.R
bacon/build
bacon/build/vignette.rds
bacon/inst
bacon/inst/CITATION
bacon/inst/doc
bacon/inst/doc/bacon.R
bacon/inst/doc/bacon.Rmd
bacon/inst/doc/bacon.html
bacon/man
bacon/man/Bacon-class.Rd
bacon/man/bacon.Rd
bacon/man/bias-methods.Rd
bacon/man/dnormmix.Rd
bacon/man/es-methods.Rd
bacon/man/estimates-methods.Rd
bacon/man/fit-methods.Rd
bacon/man/inflation-methods.Rd
bacon/man/meta-methods.Rd
bacon/man/plot-Bacon-method.Rd
bacon/man/plotnormmix.Rd
bacon/man/posteriors-methods.Rd
bacon/man/pval-methods.Rd
bacon/man/rnormmix.Rd
bacon/man/se-methods.Rd
bacon/man/topTable-methods.Rd
bacon/man/traces-methods.Rd
bacon/man/tstat-methods.Rd
bacon/src
bacon/src/Rinit.c
bacon/src/bacon.c
bacon/tests
bacon/tests/testthat
bacon/tests/testthat.R
bacon/tests/testthat/test_estimates.R
bacon/vignettes
bacon/vignettes/bacon.Rmd
bacon/vignettes/bacon.bib