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 <b>methylKit</b> 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 <code>.cov</code> files from Bismark.Alternatively, loads a pre-processed methylKit object (<code>finalmeth.RData</code>) to regenerate the methylation matrix.<b>Process Overview:</b>Reads 40 <code>.cov</code> files (CpG coverage) using <code>methRead()</code>, specifying treatment group assignments and metadata.Applies coverage filtering to remove extreme or low-confidence sites.Unites the methylation calls across samples using <code>unite()</code>.Converts to a percent methylation matrix via <code>percMethylation()</code>.Exports the resulting matrix as a tab-delimited file <code>erindata.txt</code>.<b>Inputs:</b>40 Bismark coverage files named like <code>W1.CpG_report.merged_CpG_evidence.cov</code>.Optional input: <code>finalmeth.RData</code> containing a pre-constructed <code>methylBase</code> object (<code>methBase_ob</code>).<b>Outputs:</b><code>erindata.txt</code>: a tab-separated table with columns:Sample-specific percent methylation values<code>Row_ID</code>: unique CpG identifiers in the format <code>chr_pos</code><b>Software Requirements:</b>R (≥ 4.0)Package: <code>methylKit</code> (Bioconductor)<b>Usage Notes:</b>Ensure filenames in <code>file.list</code> match the actual file names in your working directory.The <code>treatment</code> vector must be aligned with sample IDs for correct experimental grouping.CpG context only is supported (<code>context = "CpG"</code>).The script is configured for Bismark coverage format (<code>pipeline = "bismarkCoverage"</code>).Percent methylation is reported without strand collapsing (<code>destrand = FALSE</code>).