MAGAR

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

Bioconductor version: 3.24 · Package version: 1.21.0

"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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MAGAR")

Details

Maintainer	Michael Scherer <michael.scherer@dkfz.de>
Author	Michael Scherer [cre, aut] (ORCID: <https://orcid.org/0000-0001-7990-6179>)
License	GPL-3
URL	https://github.com/MPIIComputationalEpigenetics/MAGAR
Bug Reports	https://github.com/MPIIComputationalEpigenetics/MAGAR/issues
Downloads rank	404
Source branch	devel
biocViews	BatchEffect, Clustering, CopyNumberVariation, CpGIsland, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, GeneticVariability, GraphAndNetwork, ImmunoOncology, MethylSeq, MethylationArray, Microarray, Network, Preprocessing, QualityControl, Regression, SNP, Sequencing, Software, TwoChannel, mRNAMicroarray

Documentation

MAGAR: Methylation-Aware Genotype Association in R

Download

Follow the installation instructions to use this package in your R session.

Source package	MAGAR_1.21.0.tar.gz
Windows binary (x86_64)	MAGAR_1.21.0.zip
macOS binary (arm64)	MAGAR_1.21.0.tgz
macOS binary (x86_64)	MAGAR_1.21.0.tgz

Dependencies

Depends: R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm

Imports: doParallel, igraph, bigstatsr, rjson, plyr, data.table, reshape2, jsonlite, methods, UpSetR, ff, argparse, impute, RnBeads.hg19, RnBeads.hg38, utils, stats

Suggests: gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager