API Reference

The API reference is generated from the package docstrings. Rebuilding the docs is enough to pick up docstring updates.

Workflow objects

MethylSegPathway	High-level API that coordinates preparation, training, and segmentation.
MethylDataPrep	Normalize methylation input tables into the canonical SampleInfo schema.
SampleInfo	Simple container for sample metadata and prepared methylation rows.
MethylSegConfig	Lightweight helper that knows how to build a serializable dictionary from a MethylSegPathway instance and how to write/read YAML.
MethylStateAssigner	Create per-CpG window summaries and assign coarse methylation states.
MethylStateAnalyzer	Analyze learned state separation and define rule-based CpG states.
MethylSegmentor	Class to handle segmentation of methylation data using HMMs.

Enums and labels

MethylStateAssignmentMethod	Strategies for mapping emissions to biological methylation states.
MethylationStates	Canonical biological methylation states used throughout the package.
HMMType	Supported HMM model types for segmentation.

HMM backends

MethylSegHMM	Abstract base class for methylseg HMM backends.
StickyCategoricalMethylSegHMM	Categorical HMM with strong self-transition priors for smoother segments.
CTMethylSegHMM	Continuous-time HMM backend for sparsely spaced CpGs along a chromosome.

Utility helpers

get_biological_state_colors	Return a fixed biological-state palette keyed by the canonical enum values.
get_cluster_colors	Return a discrete colormap and color lookup for integer cluster labels.