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