bacon

DOI: 10.18129/B9.bioc.bacon  

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

Bioconductor version: Release (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

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

Details

biocViews	BatchEffect, Bayesian, GenomeWideAssociation, ImmunoOncology, MethylationArray, MultipleComparison, RNASeq, Regression, Software, StatisticalMethod, Transcriptomics
Version	1.28.0
In Bioconductor since	BioC 3.3 (R-3.3) (7.5 years)
License	GPL (>= 2)
Depends	R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse
Imports
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, roxygen2
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	bacon_1.28.0.tar.gz
Windows Binary	bacon_1.28.0.zip (64-bit only)
macOS Binary (x86_64)	bacon_1.28.0.tgz
macOS Binary (arm64)	bacon_1.28.0.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
Old Source Packages for BioC 3.17	Source Archive