Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Documentation for package ‘methrix’ version 1.2.06

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