Carlos Ruiz Arenas, Carles Hernández Ferrer, and Juan R Gonzalez
Summary: There is an increasing interest in the integrative analysis of the transcriptome and the methylome to understand their joint role in complex phenotypes. There have been some efforts in providing tools for integrating transcriptomics and methylomics using multivariate methods. However, there is not a common tool where integrative analyses can be performed with the most commonly used models.
Results: We introduce MEAL, an R package that enables the analysis by pairs of methylation and expression probes as well as multivariate approaches. MEAL can also analyze the global relationship between methylation and expression in a specific genomic region. The package can also analyze methylation or expression data separately, incorporating the state-of-the-art outputs and plots. It allows controlling for the effect of SNPs to avoid finding probes that can be eQTL or meQTL. To this end, new classes have been created to handle the inclusion of different omic data.
Availability and implementation: MEAL is freely avail-able as a Bioconductor package. The development version, other documentation and data used in illustrating examples can be found in BRGE web page (Bioinformatics Research Group in Epidemiology, http://www.creal.cat/brge.htm)