MAGAR

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

Bioconductor version: 3.23 · Package version: 1.20.0

"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.

Installation

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

BiocManager::install("MAGAR")

Details

Maintainer	Michael Scherer <michael.scherer@dkfz.de>
Author	Michael Scherer [cre, aut] (ORCID: <https://orcid.org/0000-0001-7990-6179>)
License	GPL-3
URL	https://github.com/MPIIComputationalEpigenetics/MAGAR
Bug Reports	https://github.com/MPIIComputationalEpigenetics/MAGAR/issues
Downloads rank	250
Source branch	RELEASE_3_23
biocViews	BatchEffect, Clustering, CopyNumberVariation, CpGIsland, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, GeneticVariability, GraphAndNetwork, ImmunoOncology, MethylSeq, MethylationArray, Microarray, Network, Preprocessing, QualityControl, Regression, SNP, Sequencing, Software, TwoChannel, mRNAMicroarray

Documentation

MAGAR: Methylation-Aware Genotype Association in R

Download

Source package

Dependencies

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

Suggests: gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager