This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see MAGAR.
Bioconductor version: 3.17
"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")
):
To install this package, start R (version "4.3") 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.
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 |
Reference Manual | ||
Text | NEWS |
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 | 1.8.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (2.5 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 |
Follow Installation instructions to use this package in your R session.
Source Package | MAGAR_1.8.0.tar.gz |
Windows Binary | MAGAR_1.8.0.zip |
macOS Binary (x86_64) | MAGAR_1.8.0.tgz |
macOS Binary (arm64) | MAGAR_1.8.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/MAGAR |
Source Repository (Developer Access) | git clone [email protected]:packages/MAGAR |
Bioc Package Browser | https://code.bioconductor.org/browse/MAGAR/ |
Package Short Url | https://bioconductor.org/packages/MAGAR/ |
Package Downloads Report | Download Stats |
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