BEclear

DOI: 10.18129/B9.bioc.BEclear    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see BEclear.

Correct for batch effects in DNA methylation data

Bioconductor version: 3.8

Provides some functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

Author: Markus Merl, Ruslan Akulenko, David Rasp

Maintainer: David Rasp <david.j.rasp at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BEclear")

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("BEclear")

 

PDF	R Script	BEclear tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, DNAMethylation, Preprocessing, Software
Version	1.14.0
In Bioconductor since	BioC 3.1 (R-3.2) (4 years)
License	GPL-2
Depends	BiocParallel(>= 1.15.12)
Imports	futile.logger, stats, Rdpack, graphics, Matrix, utils, methods, data.table (>= 1.11.8)
LinkingTo
Suggests	testthat
SystemRequirements
Enhances
URL	https://github.com/David-J-R/BEclear
BugReports	https://github.com/David-J-R/BEclear/issues
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	BEclear_1.14.0.tar.gz
Windows Binary	BEclear_1.14.0.zip
Mac OS X 10.11 (El Capitan)	BEclear_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BEclear
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BEclear
Package Short Url	http://bioconductor.org/packages/BEclear/
Package Downloads Report	Download Stats