This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Regionlevel statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.
Package details 


Author  Keegan Korthauer <[email protected]>, Sutirtha Chakraborty <[email protected]>, Yuval Benjamini <[email protected]>, Rafael Irizarry <[email protected]> 
Bioconductor views  DNAMethylation DifferentialMethylation Epigenetics FunctionalGenomics MultipleComparison Regression Sequencing Software WholeGenome 
Maintainer  Keegan Korthauer <[email protected]> 
License  MIT + file LICENSE 
Version  1.1.15 
Package repository  View on GitHub 
Installation 
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