MAGAR

DOI: 10.18129/B9.bioc.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 (3.15)

"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 "4.2") and enter:

if (!requireNamespace("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")

 

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 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 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, 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_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) MAGAR_1.3.0.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

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