MAGAR

This is the released version of MAGAR; for the devel version, see MAGAR.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

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

Bioconductor version: Release (3.23)

"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] ORCID: 0000-0001-7990-6179

Maintainer: Michael Scherer <michael.scherer at dkfz.de>

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

Michael Scherer. MAGAR: MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data. doi:10.18129/B9.bioc.MAGAR, R package version 1.20.0, https://bioconductor.org/packages/MAGAR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

BiocManager::install("MAGAR")

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

Documentation

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

browseVignettes("MAGAR")

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

Need some help? Ask on the Bioconductor Support site!

Details

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	1.20.0
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 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
System Requirements
URL	https://github.com/MPIIComputationalEpigenetics/MAGAR
Bug Reports	https://github.com/MPIIComputationalEpigenetics/MAGAR/issues

Suggests	gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager
Linking To
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Depends On Me
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Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MAGAR_1.20.0.tar.gz
Windows Binary (x86_64)	MAGAR_1.20.0.zip
macOS Binary (big-sur-x86_64)	MAGAR_1.20.0.tgz
macOS Binary (sonoma-arm64)	MAGAR_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MAGAR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MAGAR
Package Short Url	https://bioconductor.org/packages/MAGAR/
Package Downloads Report	Download Stats