Man pages for methrix
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing
| combine_methrix | Combine methrix objects |
| convert_HDF5_methrix | Converts HDF5 methrix object to standard in-memory object. |
| convert_methrix | Converts an in-memory object to an on-disk HDF5 object. |
| coverage_filter | Filter matrices by coverage |
| extract_CPGs | Extracts all CpGs from a genome |
| get_matrix | Extract methylation or coverage matrices |
| get_region_summary | Extract and summarize methylation or coverage info by regions... |
| get_stats | Estimate descriptive statistics |
| load_HDF5_methrix | Loads HDF5 methrix object |
| mask_methrix | Masks too high or too low coverage |
| methrix2bsseq | Convert 'methrix' to 'bsseq' object |
| methrix-class | Class methrix |
| methrix_data | WGBS for colon cancer, chr21 and chr22 |
| methrix_pca | Principal Component Analysis |
| methrix_report | Creates a detailed interative html summary report from... |
| order_by_sd | Order mathrix object by SD |
| plot_coverage | Coverage QC Plots |
| plot_density | Density Plot of beta-Values |
| plot_pca | Plot PCA results |
| plot_stats | Plot descriptive statistics |
| plot_violin | Violin Plot for beta-Values |
| read_bedgraphs | Versatile BedGraph reader. |
| region_filter | Filter matrices by region |
| remove_snps | Removes CpG sites from the object if they overlap with common... |
| remove_uncovered | Remove loci that are uncovered across all samples |
| save_HDF5_methrix | Saves HDF5 methrix object |
| subset_methrix | Subsets 'methrix' object based on given conditions. |
| write_bedgraphs | Writes bedGraphs from methrix object |
| write_bigwigs | Exports methrix object as bigWigs |
