.Binarize               Call Java 'BinarizeBed'
.LearnModel             Call Java 'LearnModel'
accessors               Accessors for the 'segmentation' objects
annotate_segments       Annotate segments
binarize_bam            Binarize the bam files
binarize_bed            Binarize the bed files
compare_models          Compare two or more models
count_reads_ranges      Count reads in 'GRanges' objects from bam files
emissions_file          Make emissions file name
enrichment_files        Make enrichment file names
get_frequency           Get the frequency of the segments in each cell
                        type
get_width               Get the width of the segments in each cell type
learn_model             Learn a multi-state model from chromatin data
merge_segments_bins     Merge segments and bins objects
methods                 Methods to interact with 'segmentation' objects
model_file              Make model file name
overlap_files           Make overlap file names
plot_heatmap            Visualize the model output
range_bins              Format the loaded binarized data
range_counts            Format the loaded counts data
read_bam_file           Read 'bam' files
read_bins_file          Read 'bins' files
read_cellmark_file      Read 'cellmarktable' file
read_chromsize_file     Read 'chromsizefile'
read_emissions_file     Read 'emissions' file
read_enrichment_file    Read 'enrichment' files
read_model_file         Read 'modelfile'
read_overlap_file       Read 'segments' files
read_segements_file     Read 'segments' files
read_transitions_file   Read 'transitions' file
segmentation            segmentation objects
segments_files          Make segments file names
test_obj                A segmentation object generated from the test
                        data
test_objs               A a list of segmentation objects generated from
                        the test data
tidy_ranges             Tidy the metadata of a 'GRanges' object
transitions_file        Make transitions file name
