LuxUS: DNA methylation analysis using generalized linear mixed model with spatial correlation.

ABSTRACT:

Motivation

DNA methylation is an important epigenetic modification, which has multiple functions. DNA methylation and its connections to diseases have been extensively studied in recent years. It is known that DNA methylation levels of neighboring cytosines are correlated and that differential DNA methylation typically occurs rather as regions instead of individual cytosine level.

Results

We have developed a generalized linear mixed model, LuxUS, that makes use of the correlation between neighboring cytosines to facilitate analysis of differential methylation. LuxUS implements a likelihood model for bisulfite sequencing data that accounts for experimental variation in underlying biochemistry. LuxUS can model both binary and continuous covariates, and mixed model formulation

SUBMITTER: Halla-Aho V 

PROVIDER: S-EPMC7750928 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature