LuxHS: DNA Methylation Analysis with Spatially Varying Correlation Structure

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

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.
Original languageEnglish
Title of host publicationBioinformatics and Biomedical Engineering - 8th International Work-Conference, IWBBIO 2020, Proceedings
EditorsIgnacio Rojas, Olga Valenzuela, Fernando Rojas, Luis Javier Herrera, Francisco Ortuño
Pages505-516
Number of pages12
ISBN (Electronic)978-3-030-45385-5
DOIs
Publication statusPublished - 30 Apr 2020
MoE publication typeA4 Article in a conference publication
EventInternational Work-Conference on Bioinformatics and Biomedical Engineering - Granada, Spain
Duration: 6 May 20208 May 2020

Publication series

NameLecture Notes in Computer Science
PublisherSpringer
Volume12108
ISSN (Print)0302-9743

Conference

ConferenceInternational Work-Conference on Bioinformatics and Biomedical Engineering
Abbreviated titleIWBBIO
CountrySpain
CityGranada
Period06/05/202008/05/2020

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