MAGAR

DOI: 10.18129/B9.bioc.MAGAR    

This package is for version 3.14 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: 3.14

"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>

Installation

To install this package, start R (version "4.1") 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")

 

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

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	1.2.0
In Bioconductor since	BioC 3.13 (R-4.1) (1 year)
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
LinkingTo
Suggests	gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager
SystemRequirements
Enhances
URL	https://github.com/MPIIComputationalEpigenetics/MAGAR
BugReports	https://github.com/MPIIComputationalEpigenetics/MAGAR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MAGAR_1.2.0.tar.gz
Windows Binary	MAGAR_1.2.0.zip
macOS 10.13 (High Sierra)	MAGAR_1.2.0.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