Package: dnaEPICO 0.99.22

Paul Ruiz

dnaEPICO: dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array Data

A modular and reproducible workflow for preprocessing and analysing Illumina DNA methylation array data from the EPICv2, EPIC, and 450K platforms. The package integrates quality control, probe filtering, cell-type deconvolution, phenotype preparation, generalised linear models, linear mixed-effects models, and automated report generation. It builds on established Bioconductor infrastructure and wraps commonly used tools including 'minfi', 'ENmix', and 'wateRmelon', with support for both local execution and high-performance computing workflows.

Authors:Paul Ruiz [aut, cre], Divya Mehta [aut]

dnaEPICO_0.99.22.tar.gz
dnaEPICO_0.99.22.zip(r-4.7)dnaEPICO_0.99.22.zip(r-4.6)dnaEPICO_0.99.22.zip(r-4.5)
dnaEPICO_0.99.22.tgz(r-4.6-any)dnaEPICO_0.99.22.tgz(r-4.5-any)
dnaEPICO_0.99.22.tar.gz(r-4.7-any)dnaEPICO_0.99.22.tar.gz(r-4.6-any)
dnaEPICO_0.99.22.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
dnaEPICO/json (API)
NEWS

# Install 'dnaEPICO' in R:
install.packages('dnaEPICO', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/paulyrp/dnaepico/issues

On BioConductor:dnaEPICO-0.99.20(bioc 3.24)

softwarepreprocessingmethylationarrayqualitycontrolepigeneticsmicroarraystatisticalmethodchiponchip450k-arraydna-array-methylationepic-arrayepicv2-arrayglm2illuminalmermethylationminfistatistics

5.32 score 1 stars 5 scripts 69 downloads 53 exports 195 dependencies

Last updated from:65bbf248d4. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE1491
linux-devel-x86_64OK1757
source / vignettesOK1708
linux-release-x86_64OK1652
macos-release-arm64OK1159
macos-oldrel-arm64OK1219
windows-develOK1266
windows-releaseOK1307
windows-oldrelOK1346
wasm-releaseOK1433

Exports:analyzeSvaEnmixannotateMethylationGLM_T1SummariesannotateMethylationGLMM_T1T2SummariesassessSamplesMinfiEwasWaterbuildClockFoundationInputsPreprocessingPhenobuildRawMinfiEwasWatercollectSignificantCpGsMethylationGLM_T1collectSignificantInteractionsMethylationGLMM_T1T2combineTimepointsPreprocessingPhenodnamReportestimateLCestimateLCMinfiEwasWaterestimateSvaEnmixControlsextractMakeextractMetricsMinfiEwasWaterfilterProbesMinfiEwasWaterfilterSamplesMinfiEwasWaterfitMethylationGLM_T1ModelsfitMethylationGLMM_T1T2ModelsloadMetricsPreprocessingPhenomergeSvaTargetsEnmixmethylationGLM_T1methylationGLMM_T1T2normalizeMinfiEwasWaterplotAssessmentMinfiEwasWaterplotCtrlMinfiEwasWaterplotMethylationGLM_T1DiagnosticsplotMethylationGLM_T1DistributionsplotMethylationGLMM_T1T2DiagnosticsplotMetricsMinfiEwasWaterplotNormalizationMinfiEwasWaterplotRawDensityMinfiEwasWaterplotSexMinfiEwasWaterplotSvaEnmixpredictSexMinfiEwasWaterprepareDnamReportInputsprepareMethylationGLM_T1DataprepareMethylationGLMM_T1T2DatapreprocessingMinfiEwasWaterpreprocessingPhenoreadPhenotypeTargetsreadRGSetMinfiEwasWaterrenderDnamReportsplitTimepointsPreprocessingPhenosummarizeMethylationGLM_T1ModelssummarizeMethylationGLMM_T1T2ModelssummarizeTimepointsMethylationGLMM_T1T2svaEnmixwriteMethylationGLM_T1OutputswriteMethylationGLMM_T1T2OutputswritePhenoLCMinfiEwasWaterwritePreprocessingPhenoOutputswriteSvaEnmixOutputs

Dependencies:abindaffyaffyioannotateAnnotationDbiAnnotationHubaskpassbase64beanplotBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobbootbumphuntercachemcaToolscigarilloclicliprclustercodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydoParalleldoRNGdplyrdynamicTreeCutENmixevaluateExperimentHubfarverfastmapFDb.InfiniumMethylation.hg19filelockforeachformatRfutile.loggerfutile.optionsgenefiltergeneplottergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2ggrepelglm2gluegplotsgtablegtoolsh5mreadHDF5Arrayhighrhmshttrhttr2IlluminaHumanMethylation450kanno.ilmn12.hg19illuminaioimputeIRangesirlbaisobanditeratorsjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelifecyclelimmalme4lmerTestlocfitlumimagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfiminqamulttestnleqslvnlmenloptrnor1mixnumDerivopensslopenxlsxorg.Hs.eg.dbpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRCurlRdpackreadrreformulasrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsROCRPMMRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7scalesscrimeselectrSeqinfosiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwateRmelonwithrxfunXMLxml2xtableXVectoryamlzip

dnaEPICO Overview

Paul Ruiz, Divya Mehta

Rendered fromdnaEPICO-overview.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-05-25
Started: 2026-05-23

Local Use of dnaEPICO

Paul Ruiz, Divya Mehta

Rendered fromdnaEPICO-local.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-05-23
Started: 2026-04-22

Pipeline Use of dnaEPICO

Paul Ruiz, Divya Mehta

Rendered fromdnaEPICO-pipeline.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-05-23
Started: 2026-04-22

Readme and manuals

Help Manual

Help pageTopics
Analyze surrogate variables against Sentrix chip and position factorsanalyzeSvaEnmix
Annotate one-timepoint GLM summary tables with array annotation metadataannotateMethylationGLM_T1Summaries
Annotate longitudinal mixed-effects summary tables with array annotation metadataannotateMethylationGLMM_T1T2Summaries
Assess sample quality before sample filteringassessSamplesMinfiEwasWater
Build Clock Foundation input tables from preprocessingPheno databuildClockFoundationInputsPreprocessingPheno
Build raw minfi preprocessing objectsbuildRawMinfiEwasWater
Collect significant CpG coefficient tables from fitted one-timepoint GLMscollectSignificantCpGsMethylationGLM_T1
Collect significant longitudinal model terms from fitted mixed-effects modelscollectSignificantInteractionsMethylationGLMM_T1T2
Combine selected timepoints for downstream longitudinal modelingcombineTimepointsPreprocessingPheno
dnaEPICO: DNA methylation preprocessing and modeling workflowsdnaEPICO-package dnaEPICO
Result class returned by prepareDnamReportInputsdnaEPICO_dnamReport_prepared dnaEPICO_dnamReport_prepared-class
Result class returned by renderDnamReportdnaEPICO_dnamReport_render dnaEPICO_dnamReport_render-class
Result class returned by dnamReportdnaEPICO_dnamReport dnaEPICO_dnamReport-class
Result class returned by methylationGLM_T1dnaEPICO_methylationGLM_T1 dnaEPICO_methylationGLM_T1-class
Result class returned by methylationGLMM_T1T2dnaEPICO_methylationGLMM_T1T2 dnaEPICO_methylationGLMM_T1T2-class
Result class returned by preprocessingMinfiEwasWaterdnaEPICO_preprocessingMinfiEwasWater dnaEPICO_preprocessingMinfiEwasWater-class
Result class returned by preprocessingPhenodnaEPICO_preprocessingPheno dnaEPICO_preprocessingPheno-class
Result class returned by svaEnmixdnaEPICO_svaEnmix dnaEPICO_svaEnmix-class
Generate a DNA methylation dashboard reportdnamReport
Estimate saliva cell proportions from DNA methylation beta valuesestimateLC
Estimate cell composition for preprocessingMinfiEwasWaterestimateLCMinfiEwasWater
Estimate surrogate variables from ENmix control probesestimateSvaEnmixControls
Copy dnaEPICO Makefile to a user directoryextractMake
Extract beta, M, and copy-number matrices from a filtered objectextractMetricsMinfiEwasWater
Filter probes from a normalized methylation objectfilterProbesMinfiEwasWater
Filter failed samples from an RGSet and phenotype tablefilterSamplesMinfiEwasWater
Fit CpG-wise Gaussian GLMs for one-timepoint methylation analysesfitMethylationGLM_T1Models
Fit CpG-wise mixed-effects models for longitudinal methylation analysesfitMethylationGLMM_T1T2Models
Load methylation metric matrices for preprocessingPhenoloadMetricsPreprocessingPheno
Merge surrogate variables into the phenotype tablemergeSvaTargetsEnmix
Fit CpG-wise GLMs for one-timepoint methylation analysesmethylationGLM_T1
Fit CpG-wise linear mixed-effects models for longitudinal methylation analysesmethylationGLMM_T1T2
Normalize filtered samples with minfi and wateRmelon methodsnormalizeMinfiEwasWater
Plot quality-assessment outputs for preprocessingMinfiEwasWaterplotAssessmentMinfiEwasWater
Plot ENmix control images from an RGSetplotCtrlMinfiEwasWater
Plot diagnostic summaries for one-timepoint methylation GLMsplotMethylationGLM_T1Diagnostics
Plot phenotype and covariate distributions for one-timepoint GLM analysesplotMethylationGLM_T1Distributions
Plot longitudinal mixed-effects model diagnosticsplotMethylationGLMM_T1T2Diagnostics
Plot multidimensional scaling or density summaries from final metricsplotMetricsMinfiEwasWater
Plot raw and normalized methylation distributionsplotNormalizationMinfiEwasWater
Plot raw beta-value density from a raw preprocessing objectplotRawDensityMinfiEwasWater
Plot predicted or clinical sex from 'predictSexMinfiEwasWater()'plotSexMinfiEwasWater
Plot surrogate variables for svaEnmixplotSvaEnmix
Predict biological sex from a filtered raw-data objectpredictSexMinfiEwasWater
Prepare inputs for a DNA methylation reportprepareDnamReportInputs
Prepare phenotype-plus-beta data for one-timepoint GLM analysesprepareMethylationGLM_T1Data
Prepare longitudinal phenotype-plus-beta data for mixed-effects analysesprepareMethylationGLMM_T1T2Data
Convenience preprocessing pipeline for Illumina methylation arrayspreprocessingMinfiEwasWater
Prepare phenotype and methylation matrices for downstream modelingpreprocessingPheno
Print a DNA methylation report resultprint.dnaEPICO_dnamReport
Read phenotype targets for shared dnaEPICO workflowsreadPhenotypeTargets
Read IDAT files into an annotated RGChannelSetreadRGSetMinfiEwasWater
Render a prepared DNA methylation reportrenderDnamReport
Split phenotype and methylation data by timepointsplitTimepointsPreprocessingPheno
Summarize CpG-wise Gaussian GLM fits for one-timepoint analysessummarizeMethylationGLM_T1Models
Summarize CpG-wise mixed-effects model fits for longitudinal analysessummarizeMethylationGLMM_T1T2Models
Summarize phenotype values by timepoint for longitudinal methylation analysessummarizeTimepointsMethylationGLMM_T1T2
Estimate surrogate variables from ENmix control probessvaEnmix
Write optional disk outputs for one-timepoint GLM analyseswriteMethylationGLM_T1Outputs
Write optional disk outputs for longitudinal mixed-effects analyseswriteMethylationGLMM_T1T2Outputs
Write the merged phenotype plus cell-composition tablewritePhenoLCMinfiEwasWater
Write legacy preprocessingPheno outputs to diskwritePreprocessingPhenoOutputs
Write svaEnmix outputs to diskwriteSvaEnmixOutputs