LuxHS: DNA methylation analysis with spatially varying correlation structure

Halla-aho, V.; Lähdesmäki, H.

doi:10.1101/2020.01.21.913640

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bioRxiv · 10.1101/2020.01.21.913640

LuxHS: DNA methylation analysis with spatially varying correlation structure

Halla-aho, V.·Lähdesmäki, H.

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Abstract

Bisulfite sequencing (BS-seq) is a popular method for measuring DNA methylation in basepair-resolution. Many BS-seq data analysis tools utilize the assumption of spatial correlation among the neighboring cytosines methylation states. While being a fair assumption, most existing methods leave out the possibility of deviation from the spatial correlation pattern. Our approach builds on a method which combines a generalized linear mixed model (GLMM) with a likelihood that is specific for BS-seq data and that incorporates a spatial correlation for methylation levels. We propose a novel technique using a sparsity promoting prior to enable cytosines deviating from the spatial correlation pattern. The method is tested with both simulated and real BS-seq data and compared to other differential methylation analysis tools.

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BibTeX RIS

Halla-aho, V., Lähdesmäki, H.. 2020-01-21. LuxHS: DNA methylation analysis with spatially varying correlation structure. https://doi.org/10.1101/2020.01.21.913640

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