MeDeCom: discovery and quantification of latent components of heterogeneous methylomes

Pavlo Lutsik, Martin Slawski, Gilles Gasparoni, Nikita Vedeneev, Matthias Hein, Jörn Walter

doi:10.1186/s13059-017-1182-6

MeDeCom: discovery and quantification of latent components of heterogeneous methylomes

説明

<jats:title>Abstract</jats:title> <jats:p>It is important for large-scale epigenomic studies to determine and explore the nature of hidden confounding variation, most importantly cell composition. We developed MeDeCom as a novel reference-free computational framework that allows the decomposition of complex DNA methylomes into latent methylation components and their proportions in each sample. MeDeCom is based on constrained non-negative matrix factorization with a new biologically motivated regularization function. It accurately recovers cell-type-specific latent methylation components and their proportions. MeDeCom is a new unsupervised tool for the exploratory study of the major sources of methylation variation, which should lead to a deeper understanding and better biological interpretation.</jats:p>