Package: bacon 1.41.0

Maarten van Iterson

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

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.

Authors:Maarten van Iterson [aut, cre], Erik van Zwet [ctb]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bacon/json (API)

# Install 'bacon' in R:

install.packages('bacon', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:bacon-1.41.0(bioc 3.24)bacon-1.40.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology statisticalmethod bayesian regression genomewideassociation transcriptomics rnaseq methylationarray batcheffect multiplecomparison

5.14 score 173 scripts 562 downloads 4 mentions 17 exports 26 dependencies

Last updated from:9777412674. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	173
linux-devel-arm64	NOTE	182
linux-devel-x86_64	NOTE	250
source / vignettes	OK	295
linux-release-arm64	NOTE	189
linux-release-x86_64	NOTE	278
macos-release-arm64	NOTE	114
macos-release-x86_64	NOTE	225
macos-oldrel-arm64	NOTE	96
macos-oldrel-x86_64	NOTE	177
windows-devel	NOTE	155
windows-release	NOTE	209
windows-oldrel	NOTE	186
wasm-release	OK	126

Exports:bacon bias dnormmix es estimates fit inflation meta plot plotnormmix posteriors pval rnormmix se topTable traces tstat

Dependencies:BH BiocParallel cli codetools cpp11 ellipse farver formatR futile.logger futile.options ggplot2 glue gtable isoband labeling lambda.r lifecycle R6 RColorBrewer rlang S7 scales snow vctrs viridisLite withr

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

Rendered frombacon.Rmdusingknitr::rmarkdown

Last update: 2024-04-17
Started: 2016-03-17

Citation

Development and contributors

Readme and manuals

Help Manual

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