ENmix

DOI: 10.18129/B9.bioc.ENmix    

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip

Bioconductor version: Release (3.11)

The ENmix package provides a set of quality control and data pre-processing tools for Illumina HumanMethylation450 and MethylationEPIC Beadchips. It includes ENmix background correction, RELIC dye bias correction, RCP probe-type bias adjustment, along with a number of additional tools. These functions can be used to remove unwanted experimental noise and thus to improve accuracy and reproducibility of methylation measures. ENmix functions are flexible and transparent. Users have option to choose a single pipeline command to finish all data pre-processing steps (including background correction, dye-bias adjustment, inter-array normalization and probe-type bias correction) or to use individual functions sequentially to perform data pre-processing in a more customized manner. In addition the ENmix package has selectable complementary functions for efficient data visualization (such as data distribution plots); quality control (identifing and filtering low quality data points, samples, probes, and outliers, along with imputation of missing values); identification of probes with multimodal distributions due to SNPs or other factors; exploration of data variance structure using principal component regression analysis plot; preparation of experimental factors related surrogate control variables to be adjusted in downstream statistical analysis; an efficient algorithm oxBS-MLE to estimate 5-methylcytosine and 5-hydroxymethylcytosine level; estimation of celltype proporitons; methlation age calculation and differentially methylated region (DMR) analysis.

Author: Zongli Xu [cre, aut], Liang Niu [aut], Jack Taylor [ctb]

Maintainer: Zongli Xu <xuz at niehs.nih.gov>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("ENmix")

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("ENmix")

 

PDF	R Script	ENmix User's Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylationArray, Microarray, MultiChannel, Normalization, OneChannel, Preprocessing, PrincipalComponent, QualityControl, Regression, Software, TwoChannel
Version	1.25.1
In Bioconductor since	BioC 3.1 (R-3.2) (5.5 years)
License	Artistic-2.0
Depends	parallel, doParallel, foreach, SummarizedExperiment, stats
Imports	grDevices, graphics, preprocessCore, matrixStats, methods, utils, irr, geneplotter, impute, minfi, RPMM, illuminaio, dynamicTreeCut, IRanges, Biobase, ExperimentHub, AnnotationHub, genefilter, gplots, quadprog, S4Vectors
LinkingTo
Suggests	minfiData, RUnit, BiocGenerics
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	ENmix_1.25.1.tar.gz
Windows Binary	ENmix_1.25.1.zip
macOS 10.13 (High Sierra)	ENmix_1.25.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ENmix
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ENmix
Package Short Url	https://bioconductor.org/packages/ENmix/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive