dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array Data

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Documentation for package ‘dnaEPICO’ version 0.99.30

• 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 legacy preprocessingPheno outputs to disk
writeSvaEnmixOutputs	Write svaEnmix outputs to disk