Preprocessing and Binomial Filtering of Bisulfite Sequencing Coverage Data

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