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MAGAR

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

Bioconductor version: Release (3.17)

"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 <mscherer at mpi-inf.mpg.de>

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

Installation

To install this package, start R (version "4.3") 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

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 1.8.0
In Bioconductor since BioC 3.13 (R-4.1) (2 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, utils, stats
Linking To
Suggests gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager
System Requirements
Enhances
URL https://github.com/MPIIComputationalEpigenetics/MAGAR
Bug Reports https://github.com/MPIIComputationalEpigenetics/MAGAR/issues
See More
Depends On Me
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Build Report  

Package Archives

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

Source Package MAGAR_1.8.0.tar.gz
Windows Binary MAGAR_1.8.0.zip
macOS Binary (x86_64) MAGAR_1.8.0.tgz
macOS Binary (arm64) MAGAR_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MAGAR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MAGAR
Bioc Package Browser https://code.bioconductor.org/browse/MAGAR/
Package Short Url https://bioconductor.org/packages/MAGAR/
Package Downloads Report Download Stats