Package index • dnaEPICO

All functions
`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-package` `dnaEPICO`	dnaEPICO: DNA methylation preprocessing and modeling workflows
`dnaEPICO_dnamReport-class` `dnaEPICO_dnamReport`	Result class returned by dnamReport
`dnaEPICO_dnamReport_prepared-class` `dnaEPICO_dnamReport_prepared`	Result class returned by prepareDnamReportInputs
`dnaEPICO_dnamReport_render-class` `dnaEPICO_dnamReport_render`	Result class returned by renderDnamReport
`dnaEPICO_methylationGLMM_T1T2-class` `dnaEPICO_methylationGLMM_T1T2`	Result class returned by methylationGLMM_T1T2
`dnaEPICO_methylationGLM_T1-class` `dnaEPICO_methylationGLM_T1`	Result class returned by methylationGLM_T1
`dnaEPICO_preprocessingMinfiEwasWater-class` `dnaEPICO_preprocessingMinfiEwasWater`	Result class returned by preprocessingMinfiEwasWater
`dnaEPICO_preprocessingPheno-class` `dnaEPICO_preprocessingPheno`	Result class returned by preprocessingPheno
`dnaEPICO_svaEnmix-class` `dnaEPICO_svaEnmix`	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

Reference

All functions