Package: ENmix 1.43.4

Zongli Xu

ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Tools for quanlity control, analysis and visulization of Illumina DNA methylation array data.

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

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ENmix.pdf |ENmix.html✨
ENmix/json (API)
NEWS

# Install 'ENmix' in R:

install.packages('ENmix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:ENmix-1.43.2(bioc 3.21)ENmix-1.42.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dnamethylation preprocessing qualitycontrol twochannel microarray onechannel methylationarray batcheffect normalization dataimport regression principalcomponent epigenetics multichannel differentialmethylation immunooncology

6.01 score 115 scripts 695 downloads 27 mentions 37 exports 153 dependencies

Last updated 15 days agofrom:1c378be1a5. Checks:1 OK, 1 FAILURE, 7 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 15 2025
R-4.5-win	NOTE	Mar 15 2025
R-4.5-mac	NOTE	Mar 15 2025
R-4.5-linux	NOTE	Mar 15 2025
R-4.4-win	NOTE	Mar 15 2025
R-4.4-mac	NOTE	Mar 15 2025
R-4.4-linux	NOTE	Mar 15 2025
R-4.3-win	NOTE	Mar 15 2025
R-4.3-mac	OUTDATED	Dec 28 2024

Exports:B2M calcdetP combp ctrlsva dupicc estimateCellProp freqpoly getB getCGinfo getmeth ipdmr M2B methDataSet methscore methyAge mhtplot mpreprocess multifreqpoly nmode norm.quantile oxBS.MLE p.qqplot pcrplot plotCtrl predSex preprocessENmix qcfilter QCinfo rcp rcp2 readidat readmanifest relic repicc rgDataSet rm.cgsuffix simubed

Dependencies:abind annotate AnnotationDbi AnnotationHub askpass base64 beanplot BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob bumphunter cachem caTools cli clipr cluster codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest doParallel doRNG dplyr dynamicTreeCut ExperimentHub fansi fastmap filelock foreach formatR futile.logger futile.options genefilter geneplotter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery glue gplots gtools h5mread HDF5Array hms httr httr2 illuminaio impute IRanges irlba iterators jsonlite KEGGREST KernSmooth lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime minfi multtest nlme nor1mix openssl pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools RPMM Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors scrime selectr siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs vroom withr XML xml2 xtable XVector yaml

ENmix User's Guide

Zongli Xu, Liang Niu, Jack Taylor

Rendered fromENmix.Rmdusingknitr::rmarkdownon Mar 15 2025.

Last update: 2024-06-13
Started: 2023-03-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Converting methylation beta value to M value.	B2M
To calculate detection P values	calcdetP
Identification of differentially methylated regions	combp
Non-negative internal control surrogate variables	ctrlsva
Evaluation of measurement reliability using duplicate samples	dupicc
Cell type proportion estimator	estimateCellProp
Frequency polygon plot	freqpoly
Extract methylation Beta values.	getB
CpG probe annotation inforamtion	getCGinfo
Create a methDataSet	getmeth
Differentially methylated regions	ipdmr
Converting methylation M value to beta value.	M2B
Class '"methDataSet"'	methDataSet methDataSet-class show, methDataSet-method
DNA Methylation predictors	methscore
Methylation Age estimator	methyAge
P value manhattan plot	mhtplot
methylation data QC and preprocessing pipeline for Illuminal BeadChips	mpreprocess
Multiple frequency polygon plot	multifreqpoly
Estimating number of mode for each row of data	nmode
Quantile normalization.	norm.quantile
oxBS-MLE.	oxBS.MLE
P value Q-Q plot	p.qqplot
Principal component regression plot	pcrplot
Internal control plot	plotCtrl
Estimating sample sex	predSex
The ENmix background correction	preprocessENmix
Filtering out low quality and outlier data	qcfilter
Extract QC information	QCinfo
Illumina methylation array probe type bias correction	rcp
Modified RCP method	rcp2
Parsing IDAT files for Illumina methylation arrays .	readidat
Parsing Illumina methylation arrays manifest file.	readmanifest
REgression on Logarithm of Internal Control probes (RELIC)	relic
Calculating intraclass correlation coefficient using replicate samples	repicc
Class '"rgDataSet"'	rgDataSet rgDataSet-class show, rgDataSet-method
Remove suffix from CpG names and combine duplicated CpGs	rm.cgsuffix
Simulation of bed format example file.	simubed