RNA-seq is frequently used to study allelic effects, such as imprinting, allele-specific expression and allelic imbalance. As heterozygous loci are required to study these effects, current applications typically rely on crossing inbred individuals or on prior genotyping, leading to additional work load and cost. Here, we present MAGE, Modeller of Allelic Gene Expression, which uses the Hardy-Weinberg theorem to jointly model homo- and heterozygous subjects per locus in large RNA datasets. MAGE does not require crossing or genotyping data, and can take into account minor deviation from Hardy-Weinberg equilibrium. Given sufficiently large RNA-seq datasets, MAGE can be used to detect imprinting, differential and loss of imprinting, allele-specific expression and allelic imbalance. As it largely models these effects rather than relying on simple deviation from the standard heterozygous case, it is less prone to artefacts. Moreover, MAGE provides methods to filter low quality loci and to perform quality control of loci of interest.
The MAGE package can be downloaded from GitHub (MAGE_0.1.0.tar.gz on https://github.com/Biobix/MAGE) and installed as:
install.packages(“MAGE_0.1.0.tar.gz”, repos = NULL, type=”source”)
The documenation on this package can be found on https://github.com/Biobix/MAGE/blob/master/BestPractices_imprinting.pdf