A package for detecting differential methylation. It exploits a Bayesian hidden Markov model that incorporates location dependence among genomic loci, unlike most existing methods that assume independence among observations. Bayesian priors are applied to permit information sharing across an entire chromosome for improved power of detection. The direct output of our software package is the best sequence of methylation states, eliminating the use of a subjective, and most of the time an arbitrary, threshold of pvalue for determining significance. At last, our methodology does not require replication in either or both of the two comparison groups.
Package details 


Author  Eleni Adam [aut, cre], Tieming Ji [aut], Desh Ranjan [aut] 
Bioconductor views  Bayesian BiomedicalInformatics DNAMethylation DifferentialExpression DifferentialMethylation GeneExpression HiddenMarkovModel Sequencing 
Maintainer  Eleni Adam <eadam002@odu.edu> 
License  GPL (>=2) 
Version  1.0.3 
Package repository  View on Bioconductor 
Installation 
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