Preprocessing and Binomial Filtering of Bisulfite Sequencing Coverage Data

This R script performs data preprocessing and statistical filtering on bisulfite sequencing output files (<code>*.cov</code> format) using a binomial test approach. The primary objective is to prepare methylation count data in a format compatible with the <b>DSS</b> package for downstream differential methylation analysis.The script applies a coverage threshold, computes binomial p-values against a specified background rate (default: 0.007), adjusts p-values using the Benjamini–Hochberg method, and exports three structured output files per sample:<code>_Binomial_Applied.txt</code>: Full filtered data with FDR-adjusted p-values.<code>_DSS_Format.txt</code>: Reformatted table with columns <code>chr</code>, <code>pos</code>, <code>N</code>, and <code>X</code> for DSS.<code>_w_Unique.txt</code>: Same as DSS format, with a unique site identifier column (<code>chr_pos</code>).<b>Inputs:</b>Tab-delimited coverage files matching <code>*evidence.cov</code> (e.g., from Bismark methylation extractor).Columns must include chromosome, start, end, percent methylation, count methylated (<code>C</code>), and count unmethylated (<code>T</code>).<b>Outputs:</b>For each input file:<code>[Sample]__Binomial_Applied.txt</code><code>[Sample]__DSS_Format.txt</code><code>[Sample]__w_Unique.txt</code><b>Software Requirements:</b>R (≥ 4.0)Packages: <code>readr</code>, <code>sqldf</code>, <code>doBy</code>, <code>dplyr</code>, <code>foreach</code>, <code>doParallel</code><b>Usage Notes:</b>This script is intended to run in a directory containing <code>.cov</code> files.Parallel processing is used for speed; adjust the number of cores with <code>doParallel::registerDoParallel()</code>.Downstream DSS analysis expects <code>*_DSS_Format.txt</code> files to be loaded using <code>makeBSseqData()</code>.