Package: MAGAR 1.21.0

Michael Scherer

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

"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.

Authors:Michael Scherer [cre, aut]

MAGAR_1.21.0.tar.gz
MAGAR_1.21.0.zip(r-4.7)MAGAR_1.21.0.zip(r-4.6)MAGAR_1.21.0.zip(r-4.5)
MAGAR_1.21.0.tgz(r-4.6-any)MAGAR_1.21.0.tgz(r-4.5-any)
MAGAR_1.21.0.tar.gz(r-4.7-any)MAGAR_1.21.0.tar.gz(r-4.6-any)
MAGAR_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MAGAR/json (API)
NEWS

# Install 'MAGAR' in R:
install.packages('MAGAR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mpiicomputationalepigenetics/magar/issues

On BioConductor:MAGAR-1.21.0(bioc 3.24)MAGAR-1.20.0(bioc 3.23)

regressionepigeneticsdnamethylationsnpgeneticvariabilitymethylationarraymicroarraycpgislandmethylseqsequencingmrnamicroarraypreprocessingcopynumbervariationtwochannelimmunooncologydifferentialmethylationbatcheffectqualitycontroldataimportnetworkclusteringgraphandnetwork

4.30 score 3 scripts 336 downloads 1 mentions 40 exports 191 dependencies

Last updated from:a893c77495. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE384
linux-devel-x86_64NOTE722
source / vignettesOK521
linux-release-x86_64NOTE699
macos-release-arm64NOTE539
macos-oldrel-arm64NOTE374
windows-develNOTE939
windows-releaseNOTE679
windows-oldrelNOTE981
wasm-releaseOK327

Exports:computeCorrelationBlocksdoImportdoMethQTLdoMethQTLChromosomefilterPvalgetAnnogetCorrelationBlocksgetGenogetMethDatagetOverlappingQTLgetOverlapUniversegetPhenogetResultgetResultGWASMapgetSamplesgetSpecificQTLimputeMethjoinMethQTLResultloadMethQTLInputloadMethQTLResultoverlapInputsoverlapQTLsqtlAnnotationEnrichmentqtlBaseSubstitutionEnrichmentqtlDistanceScatterplotqtlGetOptionqtlJSON2optionsqtlManhattanPlotqtlOptions2JSONqtlPlotBaseSubstitutionqtlPlotClusterSizeqtlPlotSNPCpGInteractionqtlSetOptionqtlTFBSMotifEnrichmentqtlUpsetPlotqtlUpSetPlotCorBlocksqtlUpSetPlotTagCpGsqtlVennPlotsaveMethQTLInputsaveMethQTLResult

Dependencies:abindaffyioannotateAnnotationDbiargparseaskpassbase64beanplotBHbigassertrbigparallelrbigstatsrBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemcaToolscigarilloclicliprclustercodetoolscowplotcpp11crayoncrlmmcurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdir.expirydoParalleldoRNGdotCall64dplyrellipsefarverfastmapFDb.InfiniumMethylation.hg19fffieldsfilelockfindpythonflockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegplotsgridExtragtablegtoolsh5mreadHDF5Arrayhmshttrhttr2igraphilluminaioimputeIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrmapsMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimimeminfimulttestmvtnormnlmenor1mixoligoClassesopensslorg.Hs.eg.dbparallellypillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhpcBLASctlRhtslibrjsonrlangrmioRnBeadsRnBeads.hg19RnBeads.hg38rngtoolsRsamtoolsRSpectraRSQLitertracklayerrvestS4ArraysS4VectorsS7scalesscrimeselectrSeqinfosiggenessnowsnpStatsspamSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsUpSetRutf8vctrsVGAMviridisLitevroomwithrXMLxml2xtableXVectoryaml

MAGAR: Methylation-Aware Genotype Association in R

Michael Scherer

Rendered fromMAGAR.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-10-20
Started: 2020-09-29

Readme and manuals

Help Manual

Help pageTopics
computeCorrelationBlockscomputeCorrelationBlocks
doImportdoImport
doMethQTLdoMethQTL
doMethQTLChromosomedoMethQTLChromosome
filterPvalfilterPval filterPval,MethQTLResult-method
getAnnogetAnno getAnno,methQTL-method getAnno,MethQTLInput-method getAnno,MethQTLResult-method
getCorrelationBlocksgetCorrelationBlocks getCorrelationBlocks,MethQTLResult-method
getGenogetGeno getGeno,methQTL-method getGeno,MethQTLInput-method
getMethDatagetMethData getMethData,methQTL-method getMethData,MethQTLInput-method
getOverlappingQTLgetOverlappingQTL
getOverlapUniversegetOverlapUniverse
getPhenogetPheno getPheno,methQTL-method getPheno,MethQTLInput-method
getResultgetResult getResult,MethQTLResult-method
getResultGWASMapgetResultGWASMap getResultGWASMap,MethQTLResult-method
getSamplesgetSamples getSamples,methQTL-method getSamples,MethQTLInput-method
getSpecificQTLgetSpecificQTL
imputeMethimputeMeth imputeMeth,methQTL-method imputeMeth,MethQTLInput-method
joinMethQTLResultjoinMethQTLResult
loadMethQTLInputloadMethQTLInput
loadMethQTLResultloadMethQTLResult
MethQTLInput-classMethQTLInput-class
MethQTLResult-classMethQTLResult-class
overlapInputsoverlapInputs
overlapQTLsoverlapQTLs
options.RQTL.OPTIONS
qtlAnnotationEnrichmentqtlAnnotationEnrichment
qtlBaseSubstitutionEnrichmentqtlBaseSubstitutionEnrichment
qtlDistanceScatterplotqtlDistanceScatterplot
qtlGetOption Print the value of the global optionqtlGetOption
qtlJSON2optionsqtlJSON2options
qtlManhattanPlotqtlManhattanPlot
qtlOptions2JSONqtlOptions2JSON
qtlPlotBaseSubstitutionqtlPlotBaseSubstitution
qtlPlotClusterSizeqtlPlotClusterSize
qtlPlotSNPCpGInteractionqtlPlotSNPCpGInteraction
qtlSetOptionqtlSetOption
qtlTFBSMotifEnrichmentqtlTFBSMotifEnrichment
qtlUpsetPlotqtlUpsetPlot
qtlUpSetPlotCorBlocksqtlUpSetPlotCorBlocks
qtlUpSetPlotTagCpGsqtlUpSetPlotTagCpGs
qtlVennPlotqtlVennPlot
saveMethQTLInputsaveMethQTLInput saveMethQTLInput,methQTL-method saveMethQTLInput,MethQTLInput-method
saveMethQTLResultsaveMethQTLResult saveMethQTLResult,methQTL-method saveMethQTLResult,MethQTLResult-method