Package: ENmix
Version: 1.24.0
Date: 2020-04-09
Title: Data preprocessing and quality control for Illumina
        HumanMethylation450 and MethylationEPIC BeadChip
Type: Package
Authors@R: c(person("Zongli","Xu",role=c("cre","aut"),email="xuz@niehs.nih.gov"),
    person("Liang","Niu",role=c("aut"),email="niulg@ucmail.uc.edu"),
    person("Leping","Li",role=c("ctb"),email="li3@niehs.nih.gov"),
    person("Jack","Taylor",role=c("ctb"),email="taylor@niehs.nih.gov"))
Description: 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.
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
Suggests: minfiData, RUnit, BiocGenerics
biocViews: DNAMethylation, Preprocessing, QualityControl, TwoChannel,
        Microarray, OneChannel, MethylationArray, BatchEffect,
        Normalization, DataImport, Regression,
        PrincipalComponent,Epigenetics, MultiChannel,
        DifferentialMethylation, ImmunoOncology
License: Artistic-2.0
NeedsCompilation: no
Maintainer: Zongli Xu <xuz@niehs.nih.gov>
git_url: https://git.bioconductor.org/packages/ENmix
git_branch: RELEASE_3_11
git_last_commit: 4cd647a
git_last_commit_date: 2020-04-27
Date/Publication: 2020-04-27
Packaged: 2020-04-28 01:47:34 UTC; biocbuild
Author: Zongli Xu [cre, aut],
  Liang Niu [aut],
  Leping Li [ctb],
  Jack Taylor [ctb]
Built: R 4.0.0; ; 2020-04-28 13:29:55 UTC; unix
