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MLML2R: AN R PACKAGE FOR MAXIMUM LIKELIHOOD ESTIMATION OF DNA METHYLATION AND HYDROXYMETHYLATION PROPORTIONS
Accurately measuring epigenetic marks such as DNA methylation and hydroxymethylation at the single nucleotide resolution level has increasingly become an intense focus of research in biological sciences. We introduce the R package MLML2R, which provides maximum likelihood estimates via EM-algorithm of DNA methylation and hydroxymethy-lation proportions when data from the DNA processing methods bisulfite conversion (BS), oxidative bisulfite conversion (ox-BS), and Tet-assisted bisulfite conversion (TAB) are available. For any combination of any two of the methods, we derived the exact constrained maximum likelihood estimate in analytical form, which greatly decreases analytic processing time and computational burden, common bottlenecks when processing high- throughput data. The MLML2R package is flexible as takes as input both, intensities from Infinium Methylation arrays and counts from Next Generation Sequencing technologies, and shows advantages over other available packages. Specially, we have implented for the first time in R the constrained maximum likelihood estimate of DNA methylation and hydroxymethylation from TAB data.
Maximum likelihood, DNA methylation, 5-methylcytosine, 5-hydroxymethylcytosine, MLML2R
Estatística Aplicada em Agronomia e Biologia
Samara Flamini Kiihl, Maria Tellez-Plaza, Maria José Martinez-Garrido, Arce Domingo-Relloso, José D Bermudez