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MAGAR

This is the development version of MAGAR; for the stable release version, see MAGAR.

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


Bioconductor version: Development (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 <mscherer at mpi-inf.mpg.de>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.11.0
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, utils, stats
System Requirements
URL https://github.com/MPIIComputationalEpigenetics/MAGAR
Bug Reports https://github.com/MPIIComputationalEpigenetics/MAGAR/issues
See More
Suggests gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager
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Package Archives

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

Source Package MAGAR_1.11.0.tar.gz
Windows Binary MAGAR_1.11.0.zip
macOS Binary (x86_64) MAGAR_1.11.0.tgz
macOS Binary (arm64)
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