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MeDeCom: discovery and quantification of latent components of heterogeneous methylomes.

ABSTRACT: 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.

SUBMITTER: Lutsik P

PROVIDER: S-EPMC5366155 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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MeDeCom: discovery and quantification of latent components of heterogeneous methylomes.

Lutsik Pavlo P Slawski Martin M Gasparoni Gilles G Vedeneev Nikita N Hein Matthias M Walter Jörn J

Genome biology 20170324 1

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 recove ...[more]

PMID: 28340624

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