# Perform Chromatin Segmentation Analysis in R by Calling ChromHMM

## Documentation for package ‘segmenter’ version 1.0.0

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

## Help Pages

.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
bins | Accessors for the 'segmentation' objects
bins-method | Accessors for the 'segmentation' objects
cells | Accessors for the 'segmentation' objects
cells-method | Accessors for the 'segmentation' objects
class:segmentation | segmentation objects
compare_models | Compare two or more models
counts | Accessors for the 'segmentation' objects
counts-method | Accessors for the 'segmentation' objects
count_reads_ranges | Count reads in 'GRanges' objects from bam files
emission | Accessors for the 'segmentation' objects
emission-method | Accessors for the 'segmentation' objects
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
likelihood | Accessors for the 'segmentation' objects
likelihood-method | Accessors for the 'segmentation' objects
markers | Accessors for the 'segmentation' objects
markers-method | Accessors for the 'segmentation' objects
merge_segments_bins | Merge segments and bins objects
methods | Methods to interact with 'segmentation' objects
model | Accessors for the 'segmentation' objects
model-method | Accessors for the 'segmentation' objects
model_file | Make model file name
overlap | Accessors for the 'segmentation' objects
overlap-method | Accessors for the 'segmentation' objects
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
segment | Accessors for the 'segmentation' objects
segment-method | Accessors for the 'segmentation' objects
segmentation | segmentation objects
segmentation-class | segmentation objects
segments_files | Make segments file names
show-method | Methods to interact with 'segmentation' objects
states | Accessors for the 'segmentation' objects
states-method | Accessors for the 'segmentation' objects
TES | Accessors for the 'segmentation' objects
TES-method | Accessors for the 'segmentation' objects
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
transition | Accessors for the 'segmentation' objects
transition-method | Accessors for the 'segmentation' objects
transitions_file | Make transitions file name
TSS | Accessors for the 'segmentation' objects
TSS-method | Accessors for the 'segmentation' objects