dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array Data

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Documentation for package ‘dnaEPICO’ version 0.99.20

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dnaEPICO-package dnaEPICO: DNA methylation preprocessing and modeling workflows
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 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_methylationGLMM_T1T2 Result class returned by methylationGLMM_T1T2
dnaEPICO_methylationGLMM_T1T2-class Result class returned by methylationGLMM_T1T2
dnaEPICO_methylationGLM_T1 Result class returned by methylationGLM_T1
dnaEPICO_methylationGLM_T1-class Result class returned by methylationGLM_T1
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
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