MAGAR

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see MAGAR.

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

Bioconductor version: 3.21

"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 iD ORCID: 0000-0001-7990-6179

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

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

Installation

To install this package, start R (version "4.5") 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

Version 1.16.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 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

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Package Archives

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

Source Package MAGAR_1.16.0.tar.gz

Windows Binary (x86_64) MAGAR_1.16.0.zip

macOS Binary (x86_64) MAGAR_1.16.0.tgz

macOS Binary (arm64) MAGAR_1.16.0.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/

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