API for MPIIComputationalEpigenetics/MAGAR
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
| Global functions | |
|---|---|
| MethQTLInput-class | Man page |
| MethQTLResult-class | Man page |
| QTL.OPTIONS | Man page |
| callMethQTLBlock | Source code |
| computeCorrelationBlocks | Man page Source code |
| computeRepresentativeCpG | Source code |
| doGenoImport | Source code |
| doGenoImportIDAT | Source code |
| doGenoImportImputed | Source code |
| doImport | Man page Source code |
| doImputation | Source code |
| doMethImport | Source code |
| doMethQTL | Man page Source code |
| doMethQTLChromosome | Man page Source code |
| filterPval | Man page |
| filterPval,MethQTLResult-method | Man page |
| generateFastQTLInput | Source code |
| get.value | Source code |
| getAnno | Man page |
| getAnno,MethQTLInput-method | Man page |
| getAnno,MethQTLResult-method | Man page |
| getAnno,methQTL-method | Man page |
| getCorrelationBlocks | Man page |
| getCorrelationBlocks,MethQTLResult-method | Man page |
| getGeno | Man page |
| getGeno,MethQTLInput-method | Man page |
| getGeno,methQTL-method | Man page |
| getMethData | Man page |
| getMethData,MethQTLInput-method | Man page |
| getMethData,methQTL-method | Man page |
| getOverlapUniverse | Man page Source code |
| getOverlappingQTL | Man page Source code |
| getPheno | Man page |
| getPheno,MethQTLInput-method | Man page |
| getPheno,methQTL-method | Man page |
| getResult | Man page |
| getResult,MethQTLResult-method | Man page |
| getResultGWASMap | Man page |
| getResultGWASMap,MethQTLResult-method | Man page |
| getSamples | Man page |
| getSamples,MethQTLInput-method | Man page |
| getSamples,methQTL-method | Man page |
| getSpecificQTL | Man page Source code |
| imputeMeth | Man page |
| imputeMeth,MethQTLInput-method | Man page |
| imputeMeth,methQTL-method | Man page |
| joinMethQTLResult | Man page Source code |
| loadMethQTLInput | Man page Source code |
| loadMethQTLResult | Man page Source code |
| match.assemblies | Source code |
| overlapInputs | Man page Source code |
| overlapQTLs | Man page Source code |
| parseGWASMapOutput | Source code |
| qtlAnnotationEnrichment | Man page Source code |
| qtlBaseSubstitutionEnrichment | Man page Source code |
| qtlDistanceScatterplot | Man page |
| qtlGetOption | Man page Source code |
| qtlJSON2options | Man page Source code |
| qtlLOLAEnrichment | Source code |
| qtlManhattanPlot | Man page |
| qtlOptions2JSON | Man page Source code |
| qtlPlotBaseSubstitution | Man page |
| qtlPlotClusterSize | Man page |
| qtlPlotSNPCorrelationBlock | Source code |
| qtlPlotSNPCpGInteraction | Man page Source code |
| qtlSetOption | Man page Source code |
| qtlTFBSMotifEnrichment | Man page Source code |
| qtlUpSetPlotCorBlocks | Man page |
| qtlUpSetPlotTagCpGs | Man page |
| qtlUpsetPlot | Man page |
| qtlVennPlot | Man page |
| runFastQTL | Source code |
| saveMethQTLInput | Man page |
| saveMethQTLInput,MethQTLInput-method | Man page |
| saveMethQTLInput,methQTL-method | Man page |
| saveMethQTLResult | Man page |
| saveMethQTLResult,MethQTLResult-method | Man page |
| saveMethQTLResult,methQTL-method | Man page |
| submitClusterJobs | Source code |
| submitClusterJobsSGE | Source code |
| submitClusterJobsSLURM | Source code |
