MAGAR (Methylation-Aware Genotype Association in R) is an R package for computing DNA methylation quantitative trait loci (methQTL) from DNA methylation and matched genotyping data. The tool employs a two-stage approach to compute methQTL:
The package furthermore uses established software tools for handling DNA methylation and genotyping data, including RnBeads, PLINK, and CRLMM. Thus, raw DNA methylation data (IDAT, BED files) and genotyping data (IDAT, PLINK files) can be used as input.
The package needs some Bioconductor dependencies, most notably RnBeads, which can be directly installed from the RnBeads website. Atfer instaling RnBeads, MAGAR can be installed in a R session using the devtools
package
source("https://rnbeads.org/data/install.R")
if(!requireNamespace("devtools")) install.packages("devtools")
devtools::install_github("MPIIComputationalEpigenetics/MAGAR")
You can find a detailed information for MAGAR here
Scherer, M., Gasparoni, G., Rahmouni, S. et al. Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR. Epigenetics & Chromatin 14, 44 (2021). doi:10.1186/s13072-021-00415-6
You can contact Michael Scherer for reporting bugs, feature requests or questions.
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