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 of interest
get_stats               Estimate descriptive statistics
load_HDF5_methrix       Loads HDF5 methrix object
mask_methrix            Masks too high or too low coverage
methrix-class           Class methrix
methrix2bsseq           Convert 'methrix' to 'bsseq' object
methrix_data            WGBS for colon cancer, chr21 and chr22
methrix_pca             Principal Component Analysis
methrix_report          Creates a detailed interative html summary
                        report from Methrix object
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 SNPs
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
