Package: bacon 1.35.0

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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NEWS

# Install 'bacon' in R:

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

On BioConductor:bacon-1.35.0(bioc 3.21)bacon-1.34.0(bioc 3.20)

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

5.19 score 97 scripts 498 downloads 4 mentions 17 exports 38 dependencies

Last updated 4 months agofrom:22a0e4eb75. Checks:1 OK, 10 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 28 2025
R-4.5-win-x86_64	NOTE	Jan 28 2025
R-4.5-mac-x86_64	NOTE	Jan 28 2025
R-4.5-mac-aarch64	NOTE	Jan 28 2025
R-4.5-linux-x86_64	NOTE	Jan 28 2025
R-4.4-win-x86_64	NOTE	Jan 28 2025
R-4.4-mac-x86_64	NOTE	Jan 28 2025
R-4.4-mac-aarch64	NOTE	Jan 28 2025
R-4.3-win-x86_64	NOTE	Jan 28 2025
R-4.3-mac-x86_64	NOTE	Jan 28 2025
R-4.3-mac-aarch64	NOTE	Jan 28 2025

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

Dependencies:BH BiocParallel cli codetools colorspace cpp11 ellipse fansi farver formatR futile.logger futile.options ggplot2 glue gtable isoband labeling lambda.r lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig R6 RColorBrewer rlang scales snow tibble utf8 vctrs viridisLite withr

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

Maarten van Iterson [aut, cre] and Erik van Zwet [ctb]

Rendered frombacon.Rmdusingknitr::rmarkdownon Jan 28 2025.

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