# dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array Data

## Documentation for package ‘dnaEPICO’ version 0.99.34

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

dnaEPICO-package | dnaEPICO: DNA methylation preprocessing and modeling workflows
analyzeSvaEnmix | Analyze surrogate variables against Sentrix chip and position factors
annotateMethylationGLMSummaries | Annotate one-timepoint GLM summary tables with array annotation metadata
annotateMethylationLMESummaries | Annotate longitudinal mixed-effects summary tables with array annotation metadata
assessSamplesMinfiEwasWater | Assess sample quality before sample filtering
buildClockFoundationInputsPreprocessingPheno | Build Clock Foundation input tables from preprocessingPheno data
buildRawMinfiEwasWater | Build raw minfi preprocessing objects
collectSignificantCpGsMethylationGLM | Collect significant CpG coefficient tables from fitted one-timepoint GLMs
collectSignificantInteractionsMethylationLME | Collect significant longitudinal model terms from fitted mixed-effects models
combineTimepointsPreprocessingPheno | Combine selected timepoints for downstream longitudinal modeling
dnaEPICO | dnaEPICO: DNA methylation preprocessing and modeling workflows
dnaEPICO_dnamReport | Result class returned by dnamReport
dnaEPICO_dnamReport-class | Result class returned by dnamReport
dnaEPICO_dnamReport_prepared | Result class returned by prepareDnamReportInputs
dnaEPICO_dnamReport_prepared-class | Result class returned by prepareDnamReportInputs
dnaEPICO_dnamReport_render | Result class returned by renderDnamReport
dnaEPICO_dnamReport_render-class | Result class returned by renderDnamReport
dnaEPICO_methylationGLM | Result class returned by methylationGLM
dnaEPICO_methylationGLM-class | Result class returned by methylationGLM
dnaEPICO_methylationLME | Result class returned by methylationLME
dnaEPICO_methylationLME-class | Result class returned by methylationLME
dnaEPICO_preprocessingMinfiEwasWater | Result class returned by preprocessingMinfiEwasWater
dnaEPICO_preprocessingMinfiEwasWater-class | Result class returned by preprocessingMinfiEwasWater
dnaEPICO_preprocessingPheno | Result class returned by preprocessingPheno
dnaEPICO_preprocessingPheno-class | Result class returned by preprocessingPheno
dnaEPICO_svaEnmix | Result class returned by svaEnmix
dnaEPICO_svaEnmix-class | Result class returned by svaEnmix
dnamReport | Generate a DNA methylation dashboard report
estimateLC | Estimate saliva cell proportions from DNA methylation beta values
estimateLCMinfiEwasWater | Estimate cell composition for preprocessingMinfiEwasWater
estimateSvaEnmixControls | Estimate surrogate variables from ENmix control probes
extractMake | Copy dnaEPICO Makefile to a user directory
extractMetricsMinfiEwasWater | Extract beta, M, and copy-number matrices from a filtered object
filterProbesMinfiEwasWater | Filter probes from a normalized methylation object
filterSamplesMinfiEwasWater | Filter failed samples from an RGSet and phenotype table
fitMethylationGLMModels | Fit CpG-wise Gaussian GLMs for one-timepoint methylation analyses
fitMethylationLMEModels | Fit CpG-wise mixed-effects models for longitudinal methylation analyses
loadMetricsPreprocessingPheno | Load methylation metric matrices for preprocessingPheno
mergeSvaTargetsEnmix | Merge surrogate variables into the phenotype table
methylationGLM | Fit CpG-wise GLMs for one-timepoint methylation analyses
methylationLME | Fit CpG-wise linear mixed-effects models for longitudinal methylation analyses
normalizeMinfiEwasWater | Normalize filtered samples with minfi and wateRmelon methods
plotAssessmentMinfiEwasWater | Plot quality-assessment outputs for preprocessingMinfiEwasWater
plotCtrlMinfiEwasWater | Plot ENmix control images from an RGSet
plotMethylationGLMDiagnostics | Plot diagnostic summaries for one-timepoint methylation GLMs
plotMethylationGLMDistributions | Plot phenotype and covariate distributions for one-timepoint GLM analyses
plotMethylationLMEDiagnostics | Plot longitudinal mixed-effects model diagnostics
plotMetricsMinfiEwasWater | Plot multidimensional scaling or density summaries from final metrics
plotNormalizationMinfiEwasWater | Plot raw and normalized methylation distributions
plotRawDensityMinfiEwasWater | Plot raw beta-value density from a raw preprocessing object
plotSexMinfiEwasWater | Plot predicted or clinical sex from 'predictSexMinfiEwasWater()'
plotSvaEnmix | Plot surrogate variables for svaEnmix
predictSexMinfiEwasWater | Predict biological sex from a filtered raw-data object
prepareDnamReportInputs | Prepare inputs for a DNA methylation report
prepareMethylationGLMData | Prepare phenotype-plus-methylation data for one-timepoint GLM analyses
prepareMethylationLMEData | Prepare longitudinal phenotype-plus-methylation data for mixed-effects analyses
preprocessingMinfiEwasWater | Convenience preprocessing pipeline for Illumina methylation arrays
preprocessingPheno | Prepare phenotype and methylation matrices for downstream modeling
print.dnaEPICO_dnamReport | Print a DNA methylation report result
readPhenotypeTargets | Read phenotype targets for shared dnaEPICO workflows
readRGSetMinfiEwasWater | Read IDAT files into an annotated RGChannelSet
renderDnamReport | Render a prepared DNA methylation report
splitTimepointsPreprocessingPheno | Split phenotype and methylation data by timepoint
summarizeMethylationGLMModels | Summarize CpG-wise Gaussian GLM fits for one-timepoint analyses
summarizeMethylationLMEModels | Summarize CpG-wise mixed-effects model fits for longitudinal analyses
summarizeTimepointsMethylationLME | Summarize phenotype values by timepoint for longitudinal methylation analyses
svaEnmix | Estimate surrogate variables from ENmix control probes
writeMethylationGLMOutputs | Write optional disk outputs for one-timepoint GLM analyses
writeMethylationLMEOutputs | Write optional disk outputs for longitudinal mixed-effects analyses
writePhenoLCMinfiEwasWater | Write the merged phenotype plus cell-composition table
writePreprocessingPhenoOutputs | Write preprocessingPheno outputs to disk
writeSvaEnmixOutputs | Write svaEnmix outputs to disk