| bsseq_to_edger | Convert BSseq object to edgeR methylation matrix |
| bsseq_to_log_methy_ratio | Convert BSseq object to log-methylation-ratio matrix |
| cluster_regions | Cluster regions by K-means |
| create_tabix_file | Create a tabix file using methylation calls |
| exons-method | Nanopore Methylation Result |
| exons<--method | Nanopore Methylation Result |
| exons_to_genes | Convert exon annotation to genes |
| filter_methy | Create filtered methylation file |
| get_example_exons_mus_musculus | Get example exon annotations for mus musculus (mm10) |
| get_exons | Get exon annotations |
| get_exons_hg19 | Get exon annotations |
| get_exons_hg38 | Get exon annotations |
| get_exons_homo_sapiens | Get exon annotations for Homo sapiens (hg19) |
| get_exons_mm10 | Get exon annotations |
| get_exons_mus_musculus | Get exon annotations for Mus musculus (mm10) |
| load_example_nanomethresult | Load an example NanoMethResult object |
| methy-method | Nanopore Methylation Result |
| methy<--method | Nanopore Methylation Result |
| methy_col_names | Column names for methylation data |
| methy_to_bsseq | Create BSSeq object from methylation tabix file |
| methy_to_edger | Convert NanoMethResult object to edgeR methylation matrix |
| NanoMethResult | Nanopore Methylation Result |
| NanoMethResult-class | Nanopore Methylation Result |
| plot_agg_genes | Plot gene aggregate plot |
| plot_agg_regions | Plot aggregate regions |
| plot_gene | Plot gene |
| plot_gene-method | Plot gene |
| plot_gene_heatmap | Plot gene methylation heatmap |
| plot_gene_heatmap-method | Plot gene methylation heatmap |
| plot_grange | Plot GRanges |
| plot_grange_heatmap | Plot GRanges heatmap |
| plot_mds | Plot MDS |
| plot_pca | Plot PCA |
| plot_region | Plot region |
| plot_region-method | Plot region |
| plot_region_heatmap | Plot region methylation heatmap |
| plot_region_heatmap-method | Plot region methylation heatmap |
| query_exons | Query exons |
| query_exons_gene_id | Query exons |
| query_exons_region | Query exons |
| query_exons_symbol | Query exons |
| query_methy | Query methylation data |
| region_methy_stats | Calculate region methylation statistics |
| samples-method | Nanopore Methylation Result |
| samples<--method | Nanopore Methylation Result |