Man pages for Shians/NanoMethViz
Visualise methylation data from Oxford Nanopore sequencing
| bsseq_to_edger | Convert BSseq object to edgeR methylation matrix |
| bsseq_to_log_methy_ratio | Convert BSseq object to log-methylation-ratio matrix |
| cluster_reads | Cluster reads based on methylation |
| cluster_regions | Cluster regions by K-means |
| convert_methy_format | Convert methylation calls to NanoMethViz format |
| create_tabix_file | Create a tabix file using methylation calls |
| exons | Get exon annotation |
| exons-set | Set exon annotation |
| exons_to_genes | Convert exon annotation to genes |
| filter_methy | Create filtered methylation file |
| get_cgi | Get CpG islands annotations |
| get_example_exons_mus_musculus | Get example exon annotations for mus musculus (mm10) |
| get_exons | Get exon annotations |
| get_exons_homo_sapiens | Get exon annotations for Homo sapiens (hg19) |
| get_exons_mus_musculus | Get exon annotations for Mus musculus (mm10) |
| load_example_modbamresult | Load an example ModBamResult object |
| load_example_nanomethresult | Load an example NanoMethResult object |
| methy | Get methylation data |
| methy_col_names | Column names for methylation data |
| methy-set | Set methylation data |
| methy_to_bsseq | Create BSSeq object from methylation tabix file |
| methy_to_edger | Convert NanoMethResult object to edgeR methylation matrix |
| ModBamFiles | Constructor for a ModBamFiles object |
| ModBamFiles-class | ModBamFiles class |
| ModBamResult-class | Modbam methylation results |
| modbam_to_tabix | Convert BAM with modifications to tabix format |
| mod_code | Get mod code |
| mod_code-set | Set mod code |
| NanoMethResult-class | Nanopore Methylation Result |
| NanoMethViz-package | NanoMethViz: Visualise methylation data from Oxford Nanopore... |
| plot_agg_genes | Plot gene aggregate plot |
| plot_agg_regions | Plot aggregate regions |
| plot_gene | Plot gene methylation |
| plot_gene_heatmap | 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 methylation |
| plot_region_heatmap | Plot region methylation heatmap |
| plot_violin | Plot violin for regions |
| query_exons | Query exons |
| query_methy | Query methylation data |
| raw_methy_to_tabix | Convert methylation file to tabix format |
| reexports | Objects exported from other packages |
| region_methy_stats | Calculate region methylation statistics |
| samples | Get sample annotation |
| samples-set | Set sample annotation |
| sort_methy_file | Sort methylation file |
