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

Bioconductor version: Release (3.19)

"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.

Author: Michael Scherer [cre, aut]

Maintainer: Michael Scherer <michael.scherer at>

Citation (from within R, enter citation("MAGAR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

MAGAR: Methylation-Aware Genotype Association in R HTML R Script
Reference Manual PDF


biocViews BatchEffect, Clustering, CopyNumberVariation, CpGIsland, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, GeneticVariability, GraphAndNetwork, ImmunoOncology, MethylSeq, MethylationArray, Microarray, Network, Preprocessing, QualityControl, Regression, SNP, Sequencing, Software, TwoChannel, mRNAMicroarray
Version 1.12.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm
Imports doParallel, igraph, bigstatsr, rjson, plyr, data.table, UpSetR, reshape2, jsonlite, methods, ff, argparse, impute, RnBeads.hg19, RnBeads.hg38, utils, stats
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Suggests gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager
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Follow Installation instructions to use this package in your R session.

Source Package MAGAR_1.12.0.tar.gz
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macOS Binary (x86_64) MAGAR_1.12.0.tgz
macOS Binary (arm64) MAGAR_1.12.0.tgz
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Source Repository (Developer Access) git clone
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