Introduction | Installation | Setup | Load Example Inputs | DMR Assembly from Seeds | DMR Summary | Motif Discovery | Motif-Based DMR Interactions | Visualizations | DMR Score Manhattan Plot | Single DMR Plot | Summary Circos Plot | CMEnt interactive Shiny App | Session Info

Introduction | Installation | Function Parameters | Core Input Parameters | beta | seeds | pheno | Sample Grouping Parameters | sample_group_col | casecontrol_col | ignored_sample_groups | Array and Genome Parameters | array | genome | Filtering Parameters | ext_site_delta_beta | min_seeds | min_adj_seeds | min_sites | Region Building Parameters | max_lookup_dist | expansion_window | max_bridge_seeds_gaps | max_bridge_extension_gaps | Statistical Parameters | max_pval | entanglement | testing_mode | empirical_strategy | ntries | mid_p | aggfun | Performance Parameters | njobs | verbose | Input/Output Parameters | seeds_id_col | output_prefix | beta_row_names_file | BED File Parameters | bed_provided | bed_chrom_col | bed_start_col | Annotation Parameters | annotate_with_genes | score_dmrs | Advanced Parameters | .load_debug | Global Package Options | Parallelism | Option: CMEnt.njobs | Verbosity | Option: CMEnt.verbose | Memory Management | Option: CMEnt.beta_in_mem_threshold_mb | Caching | Option: CMEnt.use_annotation_cache | Option: CMEnt.annotation_cache_dir | Option: CMEnt.jaspar_cache_dir | Motif Analysis | Option: CMEnt.jaspar_version | Option: CMEnt.jaspar_tax_group | Option: CMEnt.min_motif_similarity | Option: CMEnt.jaspar_corr_threshold | Option: CMEnt.make_debug_dir | DMR scoring | Option: CMEnt.scoring_nfold | Configuration Examples | Example 1: High-Confidence DMRs with Strict Filtering | Example 2: Broad Region Detection with Relaxed Parameters | Example 3: Empirical P-values for Small Sample Sizes | Best Practices | Troubleshooting | Issue: Out of Memory Errors | Issue: DMRs Too Small | Issue: Too Many DMRs | Issue: Slow Performance | Session Info

Scope | Build a relationship table | Map relationships to genomic features | Annotate regions | Summarise without scoring drugs | Session information

Overview | The bedMethyl format | RBedMethyl as a plug-and-play connector | Ingest a bedMethyl file | Subsetting example | Region-level summaries | Coercion to downstream classes | Session info

Overview | Installation | Loading the Package | Data Objects | Beta Values Matrix | Phenotype Data | Differentially Methylated Positions (DMPs) | Array Type | Example Analysis Workflow | Basic Data Exploration | Visualizing Methylation Differences | Examining Top DMPs | Volcano Plot of DMPs | Session Information