analyzeSvaEnmix         Analyze surrogate variables against Sentrix
                        chip and position factors
annotateMethylationGLMM_T1T2Summaries
                        Annotate longitudinal mixed-effects summary
                        tables with array annotation metadata
annotateMethylationGLM_T1Summaries
                        Annotate one-timepoint GLM 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_T1
                        Collect significant CpG coefficient tables from
                        fitted one-timepoint GLMs
collectSignificantInteractionsMethylationGLMM_T1T2
                        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-class
                        Result class returned by dnamReport
dnaEPICO_dnamReport_prepared-class
                        Result class returned by
                        prepareDnamReportInputs
dnaEPICO_dnamReport_render-class
                        Result class returned by renderDnamReport
dnaEPICO_methylationGLMM_T1T2-class
                        Result class returned by methylationGLMM_T1T2
dnaEPICO_methylationGLM_T1-class
                        Result class returned by methylationGLM_T1
dnaEPICO_preprocessingMinfiEwasWater-class
                        Result class returned by
                        preprocessingMinfiEwasWater
dnaEPICO_preprocessingPheno-class
                        Result class returned by preprocessingPheno
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
fitMethylationGLMM_T1T2Models
                        Fit CpG-wise mixed-effects models for
                        longitudinal methylation analyses
fitMethylationGLM_T1Models
                        Fit CpG-wise Gaussian GLMs for one-timepoint
                        methylation analyses
loadMetricsPreprocessingPheno
                        Load methylation metric matrices for
                        preprocessingPheno
mergeSvaTargetsEnmix    Merge surrogate variables into the phenotype
                        table
methylationGLMM_T1T2    Fit CpG-wise linear mixed-effects models for
                        longitudinal methylation analyses
methylationGLM_T1       Fit CpG-wise GLMs for one-timepoint 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
plotMethylationGLMM_T1T2Diagnostics
                        Plot longitudinal mixed-effects model
                        diagnostics
plotMethylationGLM_T1Diagnostics
                        Plot diagnostic summaries for one-timepoint
                        methylation GLMs
plotMethylationGLM_T1Distributions
                        Plot phenotype and covariate distributions for
                        one-timepoint GLM analyses
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
prepareMethylationGLMM_T1T2Data
                        Prepare longitudinal phenotype-plus-beta data
                        for mixed-effects analyses
prepareMethylationGLM_T1Data
                        Prepare phenotype-plus-beta data for
                        one-timepoint GLM 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
summarizeMethylationGLMM_T1T2Models
                        Summarize CpG-wise mixed-effects model fits for
                        longitudinal analyses
summarizeMethylationGLM_T1Models
                        Summarize CpG-wise Gaussian GLM fits for
                        one-timepoint analyses
summarizeTimepointsMethylationGLMM_T1T2
                        Summarize phenotype values by timepoint for
                        longitudinal methylation analyses
svaEnmix                Estimate surrogate variables from ENmix control
                        probes
writeMethylationGLMM_T1T2Outputs
                        Write optional disk outputs for longitudinal
                        mixed-effects analyses
writeMethylationGLM_T1Outputs
                        Write optional disk outputs for one-timepoint
                        GLM analyses
writePhenoLCMinfiEwasWater
                        Write the merged phenotype plus
                        cell-composition table
writePreprocessingPhenoOutputs
                        Write legacy preprocessingPheno outputs to disk
writeSvaEnmixOutputs    Write svaEnmix outputs to disk
