To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ENmix")
In most cases, you don't need to download the package archive at all.
ENmix
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Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Bioconductor version: Release (3.5)
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("https://bioconductor.org/biocLite.R")
biocLite("ENmix")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ENmix")
| R Script | ENmix User's Guide | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | BatchEffect, DNAMethylation, DataImport, MethylationArray, Microarray, Normalization, OneChannel, Preprocessing, PrincipalComponent, QualityControl, Regression, Software, TwoChannel |
| Version | 1.12.4 |
| 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.
| Source Package | ENmix_1.12.4.tar.gz |
| Windows Binary | ENmix_1.12.4.zip |
| Mac OS X 10.11 (El Capitan) | ENmix_1.12.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ENmix |
| Package Short Url | http://bioconductor.org/packages/ENmix/ |
| Package Downloads Report | Download Stats |
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