To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ENmix")

In most cases, you don't need to download the package archive at all.

ENmix

 

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

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip

Bioconductor version: Development (3.6)

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; and an efficient algorithm oxBS-MLE to estimate 5-methylcytosine and 5-hydroxymethylcytosine level.

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

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ENmix")

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, MethylationArray, Microarray, Normalization, OneChannel, Preprocessing, PrincipalComponent, QualityControl, Regression, Software, TwoChannel
Version 1.13.8
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
License Artistic-2.0
Depends parallel, doParallel, foreach, SummarizedExperiment(>= 1.1.6), minfi(>= 1.22.0)
Imports MASS, preprocessCore, wateRmelon, sva, geneplotter, impute, grDevices, graphics, stats
LinkingTo
Suggests minfiData(>= 0.4.1), RPMM, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source ENmix_1.13.8.tar.gz
Windows Binary ENmix_1.13.8.zip
Mac OS X 10.11 (El Capitan) ENmix_1.13.8.tgz
Source Repository git clone https://git.bioconductor.org/packages/ENmix
Package Short Url http://bioconductor.org/packages/ENmix/
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