jDMRgrid is an essential tool for conducting efficient and heuristic DMR (Differentially Methylated Region) calling in large-scale epigenomic studies involving population-level analyses and control/treatment experiments. Its functionality relies on a grid-based methodology that involves dividing the genome into sliding windows or bins of customizable sizes. It determines methylation state calls for each individual sliding window based on a Hidden Markov Model (HMM) approach. Subsequently, these calls are consolidated into a matrix format by merging data from all samples. Additionally, user can perform a filtration of DMR matrix to remove non-polymorphic patterns from the merged matrix.

To install from GitHub (development version), follow the steps given below.

install.packages("devtools")
library(devtools)
devtools::install_github("jlaab-code/jDMR")

Please open the vignette file.