bacon

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see bacon.

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

Bioconductor version: 3.14

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 "4.1") 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")

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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, Bayesian, GenomeWideAssociation, ImmunoOncology, MethylationArray, MultipleComparison, RNASeq, Regression, Software, StatisticalMethod, Transcriptomics

Version 1.22.0

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

Suggests BiocStyle, knitr, rmarkdown, testthat, roxygen2

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package bacon_1.22.0.tar.gz

Windows Binary bacon_1.22.0.zip (32- & 64-bit)

macOS 10.13 (High Sierra) bacon_1.22.0.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 3.14 Source Archive