Index

_

__init__() (methylseg.CTMethylSegHMM method) (methylseg.HMMType method) (methylseg.MethylationStates method) (methylseg.MethylDataPrep method) (methylseg.MethylSegConfig method) (methylseg.MethylSegHMM method) (methylseg.MethylSegmentor method) (methylseg.MethylSegPathway method) (methylseg.MethylStateAnalyzer method) (methylseg.MethylStateAssigner method) (methylseg.MethylStateAssignmentMethod method) (methylseg.SampleInfo method) (methylseg.StickyCategoricalMethylSegHMM method)

A

apply_kmeans_to_emissions() (methylseg.MethylStateAssigner method) apply_kmeans_to_sample() (methylseg.MethylStateAssigner method)

assign_states() (methylseg.MethylSegmentor method) AUTO (methylseg.MethylStateAssignmentMethod attribute)

B

build_emission_matrix() (methylseg.MethylStateAssigner method)

build_pathway() (methylseg.MethylSegConfig method)

C

calculate_kmeans_cluster_metrics() (methylseg.MethylStateAssigner method) COMMON_ALIASES (methylseg.MethylDataPrep attribute) convert_to_numeric() (methylseg.MethylationStates static method) create_model() (methylseg.CTMethylSegHMM method) (methylseg.MethylSegHMM method) (methylseg.StickyCategoricalMethylSegHMM method)

create_regions() (methylseg.MethylSegmentor method) CT (methylseg.HMMType attribute) CTMethylSegHMM (class in methylseg)

D

DEFAULT_STAY_PROB (methylseg.StickyCategoricalMethylSegHMM attribute) define_states_by_rules() (methylseg.MethylStateAnalyzer method)

define_states_by_rules_param() (methylseg.MethylStateAnalyzer method) DEFINITION (methylseg.MethylStateAssignmentMethod attribute)

E

EMISSION_MISMATCH_PROB (methylseg.StickyCategoricalMethylSegHMM attribute)

evaluate_clustering_concordance() (methylseg.MethylStateAnalyzer method) evaluate_rules_against_kmeans() (methylseg.MethylStateAnalyzer method)

F

fit() (methylseg.CTMethylSegHMM method) (methylseg.MethylSegHMM method) (methylseg.StickyCategoricalMethylSegHMM method) fit_kmeans_on_emissions() (methylseg.MethylStateAssigner method) fit_pathway() (methylseg.MethylSegPathway method) format_fit() (methylseg.CTMethylSegHMM method) (methylseg.MethylSegHMM method) (methylseg.StickyCategoricalMethylSegHMM method)

format_predict() (methylseg.CTMethylSegHMM method) (methylseg.MethylSegHMM method) (methylseg.StickyCategoricalMethylSegHMM method) from_instance() (methylseg.MethylSegConfig class method) from_yaml() (methylseg.MethylSegConfig class method) (methylseg.MethylSegPathway class method)

G

generate_regions() (methylseg.MethylSegPathway method) get_biological_state_colors() (in module methylseg) get_clean_regions() (methylseg.MethylSegPathway method)

get_cluster_colors() (in module methylseg) get_pca_loadings() (methylseg.MethylStateAssigner method) get_pretrained_model() (methylseg.MethylSegPathway class method) get_state_cutoffs() (methylseg.MethylSegConfig method)

H

HEADER_ALIASES (methylseg.MethylDataPrep attribute)

HIGH (methylseg.MethylationStates attribute) HMMType (class in methylseg)

I

INPUT_ROW_INDEX_COL (methylseg.MethylDataPrep attribute)

INTERMEDIATE (methylseg.MethylationStates attribute)

K

KMEANS (methylseg.MethylStateAssignmentMethod attribute)

L

LOW (methylseg.MethylationStates attribute)

LOW_COVERAGE_LIKE_BETA_VALUES (methylseg.MethylDataPrep attribute)

M

make_emissionprob() (methylseg.StickyCategoricalMethylSegHMM method) make_sticky_transmat() (methylseg.StickyCategoricalMethylSegHMM method) meth_data (methylseg.SampleInfo attribute) MethylationStates (class in methylseg) MethylDataPrep (class in methylseg) MethylSegConfig (class in methylseg)

MethylSegHMM (class in methylseg) MethylSegmentor (class in methylseg) MethylSegPathway (class in methylseg) MethylStateAnalyzer (class in methylseg) MethylStateAssigner (class in methylseg) MethylStateAssignmentMethod (class in methylseg)

O

optimize_rule_params_random() (methylseg.MethylStateAnalyzer method)

P

plot_embedding() (methylseg.MethylSegPathway method) (methylseg.MethylStateAssigner method) plot_feature_distributions_by_kmeans_state() (methylseg.MethylStateAssigner method) plot_kmeans_clusters() (methylseg.MethylStateAssigner method) plot_labels() (methylseg.MethylSegmentor method) (methylseg.MethylSegPathway method) (methylseg.MethylStateAnalyzer method) (methylseg.MethylStateAssigner method) plot_pca_clusters() (methylseg.MethylStateAssigner method) plot_pca_clusters_with_region() (methylseg.MethylStateAssigner method) plot_train_pca_clusters() (methylseg.MethylStateAssigner method)

plot_training_embedding() (methylseg.MethylStateAssigner method) plot_umap_clusters() (methylseg.MethylStateAssigner method) PMD (methylseg.MethylationStates attribute) predict() (methylseg.CTMethylSegHMM method) (methylseg.MethylSegHMM method) (methylseg.StickyCategoricalMethylSegHMM method) prepare() (methylseg.MethylDataPrep method) prepare_dataframe() (methylseg.MethylDataPrep method) prepare_sample_for_clustering() (methylseg.MethylStateAssigner method) prepare_sample_info() (methylseg.MethylSegPathway static method) preprocess_emission_features() (methylseg.MethylStateAssigner method) pretty_print_rules() (methylseg.MethylStateAnalyzer method)

R

regions_to_bed() (methylseg.MethylSegmentor method) REQUIRED_COLUMNS (methylseg.MethylDataPrep attribute) resolution (methylseg.SampleInfo attribute)

resolve_feature_cols() (methylseg.MethylStateAssigner method) rewrite_artifact_paths() (methylseg.MethylSegConfig method) run_on_all_chroms() (methylseg.MethylSegPathway method) run_pathway() (methylseg.MethylSegPathway method)

S

sample_id (methylseg.SampleInfo attribute) SampleInfo (class in methylseg) segment_sample() (methylseg.MethylSegmentor method) set_out_dir() (methylseg.MethylSegPathway method)

set_state_cutoffs() (methylseg.MethylStateAnalyzer method) set_state_cutoffs_from_yaml() (methylseg.MethylStateAnalyzer method) STICKY (methylseg.HMMType attribute) StickyCategoricalMethylSegHMM (class in methylseg) subset_sample_info_by_chroms() (methylseg.MethylSegPathway static method)

T

to_yaml() (methylseg.MethylSegConfig method) (methylseg.MethylSegPathway method)

train_kmeans_for_sample() (methylseg.MethylStateAssigner method) TRANSITION_PRIOR_STRENGTH (methylseg.StickyCategoricalMethylSegHMM attribute)

W

write_prepared_tsv() (methylseg.MethylDataPrep method)