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 1.12.0
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 |