Package: MAGAR 1.15.0

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_1.15.0.tar.gz
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MAGAR_1.15.0.tgz(r-4.4-any)MAGAR_1.15.0.tgz(r-4.3-any)
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MAGAR.pdf |MAGAR.html✨
MAGAR/json (API)
NEWS

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

Peer review:

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

On BioConductor:MAGAR-1.13.0(bioc 3.20)MAGAR-1.12.0(bioc 3.19)

regressionepigeneticsdnamethylationsnpgeneticvariabilitymethylationarraymicroarraycpgislandmethylseqsequencingmrnamicroarraypreprocessingcopynumbervariationtwochannelimmunooncologydifferentialmethylationbatcheffectqualitycontroldataimportnetworkclusteringgraphandnetwork

4.60 score 3 scripts 274 downloads 1 mentions 40 exports 190 dependencies

Last updated 23 days agofrom:dc99db85fd. Checks:OK: 1 ERROR: 2 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winERROROct 31 2024
R-4.5-linuxERROROct 31 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:computeCorrelationBlocksdoImportdoMethQTLdoMethQTLChromosomefilterPvalgetAnnogetCorrelationBlocksgetGenogetMethDatagetOverlappingQTLgetOverlapUniversegetPhenogetResultgetResultGWASMapgetSamplesgetSpecificQTLimputeMethjoinMethQTLResultloadMethQTLInputloadMethQTLResultoverlapInputsoverlapQTLsqtlAnnotationEnrichmentqtlBaseSubstitutionEnrichmentqtlDistanceScatterplotqtlGetOptionqtlJSON2optionsqtlManhattanPlotqtlOptions2JSONqtlPlotBaseSubstitutionqtlPlotClusterSizeqtlPlotSNPCpGInteractionqtlSetOptionqtlTFBSMotifEnrichmentqtlUpsetPlotqtlUpSetPlotCorBlocksqtlUpSetPlotTagCpGsqtlVennPlotsaveMethQTLInputsaveMethQTLResult

Dependencies:abindaffyioannotateAnnotationDbiargparseaskpassbase64beanplotBHbigassertrbigparallelrbigstatsrBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemcaToolsclicliprclustercodetoolscolorspacecowplotcpp11crayoncrlmmcurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdoParalleldoRNGdotCall64dplyrellipsefansifarverfastmapFDb.InfiniumMethylation.hg19fffieldsfindpythonflockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegplotsgridExtragtablegtoolsHDF5Arrayhmshttrhttr2igraphilluminaioimputeIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrmapsMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimulttestmunsellmvtnormnlmenor1mixoligoClassesopensslorg.Hs.eg.dbparallellypillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhpcBLASctlRhtslibrjsonrlangrmioRnBeadsRnBeads.hg19RnBeads.hg38rngtoolsRsamtoolsRSpectraRSQLitertracklayerrvestS4ArraysS4VectorsscalesscrimeselectrsiggenessnowsnpStatsspamSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsUpSetRutf8vctrsVGAMviridisLitevroomwithrXMLxml2xtableXVectoryamlzlibbioc

MAGAR: Methylation-Aware Genotype Association in R

Michael Scherer

Rendered fromMAGAR.Rmdusingknitr::rmarkdownon Oct 30 2024.

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