MethQTLInput-class      MethQTLInput-class
MethQTLResult-class     MethQTLResult-class
QTL.OPTIONS             options.R
computeCorrelationBlocks
                        computeCorrelationBlocks
doImport                doImport
doMethQTL               doMethQTL
doMethQTLChromosome     doMethQTLChromosome
filterPval,MethQTLResult-method
                        filterPval
getAnno,MethQTLInput-method
                        getAnno
getCorrelationBlocks,MethQTLResult-method
                        getCorrelationBlocks
getGeno,MethQTLInput-method
                        getGeno
getMethData,MethQTLInput-method
                        getMethData
getOverlapUniverse      getOverlapUniverse
getOverlappingQTL       getOverlappingQTL
getPheno,MethQTLInput-method
                        getPheno
getResult,MethQTLResult-method
                        getResult
getResultGWASMap,MethQTLResult-method
                        getResultGWASMap
getSamples,MethQTLInput-method
                        getSamples
getSpecificQTL          getSpecificQTL
imputeMeth,MethQTLInput-method
                        imputeMeth
joinMethQTLResult       joinMethQTLResult
loadMethQTLInput        loadMethQTLInput
loadMethQTLResult       loadMethQTLResult
overlapInputs           overlapInputs
overlapQTLs             overlapQTLs
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
qtlUpSetPlotCorBlocks   qtlUpSetPlotCorBlocks
qtlUpSetPlotTagCpGs     qtlUpSetPlotTagCpGs
qtlUpsetPlot            qtlUpsetPlot
qtlVennPlot             qtlVennPlot
saveMethQTLInput,MethQTLInput-method
                        saveMethQTLInput
saveMethQTLResult,MethQTLResult-method
                        saveMethQTLResult
