ENmix
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see ENmix.
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Bioconductor version: 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>
citation("ENmix")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("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")| ENmix User's Guide | R Script | |
| Reference Manual | ||
| NEWS | Text |
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) (9 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 |
| System Requirements | |
| URL |
See More
| Suggests | minfiData, RUnit, BiocGenerics |
| 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 | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ENmix/ |
| Package Short Url | https://bioconductor.org/packages/ENmix/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |