MAGAR
An R package to compute methylation quantitative trait loci (methQTL) from DNA methylation and genotyping data.
Science Score: 36.0%
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Low similarity (11.7%) to scientific vocabulary
Repository
An R package to compute methylation quantitative trait loci (methQTL) from DNA methylation and genotyping data.
Basic Info
- Host: GitHub
- Owner: MPIIComputationalEpigenetics
- Language: R
- Default Branch: master
- Size: 148 MB
Statistics
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
MAGAR
Short description
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:
- CpG correlation blocks are computed to mimic DNA methylation haplotypes. The correlation blocks are computed from CpGs that are highly correlated across the samples.
- For each correlation block, a representative CpG (tag-CpG) is computed and used in a linear modeling strategy (or alternatively with fastQTL) to determine significant associations between genotype variation and changes in DNA methylation of particular CpGs.
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.
Installation
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
r
source("https://rnbeads.org/data/install.R")
if(!requireNamespace("devtools")) install.packages("devtools")
devtools::install_github("MPIIComputationalEpigenetics/MAGAR")
Documentation
You can find a detailed information for MAGAR here
Citation
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
Contact
You can contact Michael Scherer for reporting bugs, feature requests or questions.
Owner
- Name: Computational Epigenetics Group at Max-Planck-Institut für Informatik
- Login: MPIIComputationalEpigenetics
- Kind: organization
- Email: felipe.albrecht@mpi-inf.mpg.de
- Location: Saarbrücken, Germany
- Website: http://www.computational-epigenetics.de/
- Repositories: 17
- Profile: https://github.com/MPIIComputationalEpigenetics
Computational Epigenetics Group / Computational Biology and Applied Algorithmics / Max-Planck-Institut für Informatik
GitHub Events
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- Push event: 1
- Create event: 1
Last Year
- Push event: 1
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Michael Scherer | s****r@g****m | 122 |
| schmic05 | m****r@m****e | 27 |
| Michael Scherer | m****r@l****6 | 4 |
| Nitesh Turaga | n****a@g****m | 4 |
| Michael | m****r@l****e | 1 |
Committer Domains (Top 20 + Academic)
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Packages
- Total packages: 1
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Total downloads:
- bioconductor 8,495 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: MAGAR
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
- Homepage: https://github.com/MPIIComputationalEpigenetics/MAGAR
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/MAGAR/inst/doc/MAGAR.pdf
- License: GPL-3
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Latest release: 1.16.0
published about 1 year ago