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


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Documentation for package ‘MAGAR’ version 1.6.0

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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