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bacon

This is the development version of bacon; for the stable release version, see bacon.

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


Bioconductor version: Development (3.19)

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]

Maintainer: Maarten van Iterson <mviterson at gmail.com>

Citation (from within R, enter citation("bacon")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("bacon")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("bacon")
Controlling bias and inflation in association studies using the empirical null distribution HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, Bayesian, GenomeWideAssociation, ImmunoOncology, MethylationArray, MultipleComparison, RNASeq, Regression, Software, StatisticalMethod, Transcriptomics
Version 1.31.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL (>= 2)
Depends R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse
Imports
System Requirements
URL
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Suggests BiocStyle, knitr, rmarkdown, testthat, roxygen2
Linking To
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package bacon_1.31.0.tar.gz
Windows Binary bacon_1.31.0.zip
macOS Binary (x86_64) bacon_1.31.0.tgz
macOS Binary (arm64) bacon_1.31.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/bacon
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bacon
Bioc Package Browser https://code.bioconductor.org/browse/bacon/
Package Short Url https://bioconductor.org/packages/bacon/
Package Downloads Report Download Stats