# Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

## Documentation for package ‘methrix’ version 1.0.05

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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 methrix
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