Generation of Genome-Wide Methylation Matrix from Bismark Coverage Files Using methylKit

This R script processes bisulfite sequencing coverage files generated by the Bismark methylation extractor and produces a comprehensive CpG methylation matrix using the methylKit package. The matrix reports the percentage methylation for each CpG site across all samples, formatted for downstream statistical analysis and visualization.
The script includes two pipelines:
Reads and filters raw .cov files from Bismark.Alternatively, loads a pre-processed methylKit object (finalmeth.RData) to regenerate the methylation matrix.Process Overview:Reads 40 .cov files (CpG coverage) using methRead(), specifying treatment group assignments and metadata.Applies coverage filtering to remove extreme or low-confidence sites.Unites the methylation calls across samples using unite().Converts to a percent methylation matrix via percMethylation().Exports the resulting matrix as a tab-delimited file erindata.txt.Inputs:40 Bismark coverage files named like W1.CpG_report.merged_CpG_evidence.cov.Optional input: finalmeth.RData containing a pre-constructed methylBase object (methBase_ob).Outputs:erindata.txt: a tab-separated table with columns:Sample-specific percent methylation valuesRow_ID: unique CpG identifiers in the format chr_posSoftware Requirements:R (≥ 4.0)Package: methylKit (Bioconductor)Usage Notes:Ensure filenames in file.list match the actual file names in your working directory.The treatment vector must be aligned with sample IDs for correct experimental grouping.CpG context only is supported (context = "CpG").The script is configured for Bismark coverage format (pipeline = "bismarkCoverage").Percent methylation is reported without strand collapsing (destrand = FALSE).