# MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

## Documentation for package ‘MAGAR’ version 1.19.0

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

## Help Pages

computeCorrelationBlocks | computeCorrelationBlocks
doImport | doImport
doMethQTL | doMethQTL
doMethQTLChromosome | doMethQTLChromosome
filterPval | filterPval
filterPval-method | filterPval
getAnno | getAnno
getAnno-method | getAnno
getCorrelationBlocks | getCorrelationBlocks
getCorrelationBlocks-method | getCorrelationBlocks
getGeno | getGeno
getGeno-method | getGeno
getMethData | getMethData
getMethData-method | getMethData
getOverlappingQTL | getOverlappingQTL
getOverlapUniverse | getOverlapUniverse
getPheno | getPheno
getPheno-method | getPheno
getResult | getResult
getResult-method | getResult
getResultGWASMap | getResultGWASMap
getResultGWASMap-method | getResultGWASMap
getSamples | getSamples
getSamples-method | getSamples
getSpecificQTL | getSpecificQTL
imputeMeth | imputeMeth
imputeMeth-method | imputeMeth
joinMethQTLResult | joinMethQTLResult
loadMethQTLInput | loadMethQTLInput
loadMethQTLResult | loadMethQTLResult
MethQTLInput-class | MethQTLInput-class
MethQTLResult-class | MethQTLResult-class
overlapInputs | overlapInputs
overlapQTLs | overlapQTLs
QTL.OPTIONS | options.R
qtlAnnotationEnrichment | qtlAnnotationEnrichment
qtlBaseSubstitutionEnrichment | qtlBaseSubstitutionEnrichment
qtlDistanceScatterplot | qtlDistanceScatterplot
qtlGetOption | qtlGetOption Print the value of the global option
qtlJSON2options | qtlJSON2options
qtlManhattanPlot | qtlManhattanPlot
qtlOptions2JSON | qtlOptions2JSON
qtlPlotBaseSubstitution | qtlPlotBaseSubstitution
qtlPlotClusterSize | qtlPlotClusterSize
qtlPlotSNPCpGInteraction | qtlPlotSNPCpGInteraction
qtlSetOption | qtlSetOption
qtlTFBSMotifEnrichment | qtlTFBSMotifEnrichment
qtlUpsetPlot | qtlUpsetPlot
qtlUpSetPlotCorBlocks | qtlUpSetPlotCorBlocks
qtlUpSetPlotTagCpGs | qtlUpSetPlotTagCpGs
qtlVennPlot | qtlVennPlot
saveMethQTLInput | saveMethQTLInput
saveMethQTLInput-method | saveMethQTLInput
saveMethQTLResult | saveMethQTLResult
saveMethQTLResult-method | saveMethQTLResult