computeCorrelationBlocks	computeCorrelationBlocks
doImport	doImport
doMethQTL	doMethQTL
doMethQTLChromosome	doMethQTLChromosome
filterPval	filterPval
filterPval,MethQTLResult-method	filterPval
getAnno	getAnno
getAnno,methQTL-method	getAnno
getAnno,MethQTLInput-method	getAnno
getAnno,MethQTLResult-method	getAnno
getCorrelationBlocks	getCorrelationBlocks
getCorrelationBlocks,MethQTLResult-method	getCorrelationBlocks
getGeno	getGeno
getGeno,methQTL-method	getGeno
getGeno,MethQTLInput-method	getGeno
getMethData	getMethData
getMethData,methQTL-method	getMethData
getMethData,MethQTLInput-method	getMethData
getOverlappingQTL	getOverlappingQTL
getOverlapUniverse	getOverlapUniverse
getPheno	getPheno
getPheno,methQTL-method	getPheno
getPheno,MethQTLInput-method	getPheno
getResult	getResult
getResult,MethQTLResult-method	getResult
getResultGWASMap	getResultGWASMap
getResultGWASMap,MethQTLResult-method	getResultGWASMap
getSamples	getSamples
getSamples,methQTL-method	getSamples
getSamples,MethQTLInput-method	getSamples
getSpecificQTL	getSpecificQTL
imputeMeth	imputeMeth
imputeMeth,methQTL-method	imputeMeth
imputeMeth,MethQTLInput-method	imputeMeth
joinMethQTLResult	joinMethQTLResult
loadMethQTLInput	loadMethQTLInput
loadMethQTLResult	loadMethQTLResult
MethQTLInput-class	MethQTLInput-class
MethQTLResult-class	MethQTLResult-class
overlapInputs	overlapInputs
overlapQTLs	overlapQTLs
QTL.OPTIONS	QTL.OPTIONS
qtlAnnotationEnrichment	qtlAnnotationEnrichment
qtlBaseSubstitutionEnrichment	qtlBaseSubstitutionEnrichment
qtlDistanceScatterplot	qtlDistanceScatterplot
qtlGetOption	qtlGetOption
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,methQTL-method	saveMethQTLInput
saveMethQTLInput,MethQTLInput-method	saveMethQTLInput
saveMethQTLResult	saveMethQTLResult
saveMethQTLResult,methQTL-method	saveMethQTLResult
saveMethQTLResult,MethQTLResult-method	saveMethQTLResult
