Index

B

BetaBinomialMixture (class in prism.mixture)

bic() (prism.mixture.BetaBinomialMixture method)

C

character_indices() (in module prism.extract)

common_intersection() (in module prism.deconvolute)

D

discard_noninformative_reads() (in module prism.extract)

dispersions_ (prism.mixture.BetaBinomialMixture attribute)

E

extend_region() (in module prism.extract)

extract_chromosome() (in module prism.util)

F

fit() (prism.mixture.BetaBinomialMixture method)

G

get_bam_handle() (in module prism.util) get_binary_string_representation() (in module prism.util) get_chromosome() (in module prism.deconvolute) get_common_headers_by_jaccard_similarity() (in module prism.util) get_counts() (prism.mixture.BetaBinomialMixture method) get_cpg_coordinates() (in module prism.extract) get_depths() (prism.mixture.BetaBinomialMixture method)

get_dispersions() (prism.mixture.BetaBinomialMixture method) get_headers() (prism.mixture.BetaBinomialMixture method) get_means() (prism.mixture.BetaBinomialMixture method) get_n_components() (prism.mixture.BetaBinomialMixture method) get_n_dimensions() (prism.mixture.BetaBinomialMixture method) get_subclone_assignment() (in module prism.deconvolute) get_weights() (prism.mixture.BetaBinomialMixture method)

H

has_overlap() (in module prism.extract)

hmm_proba() (in module prism.proofreading) HMMModel (class in prism.hmm)

I

identify_subclone() (in module prism.deconvolute)

is_fully_methylated_or_unmethylated() (in module prism.util) is_methylated() (in module prism.hmm)

J

jaccard_similarity() (in module prism.util)

M

mark_outlier_clusters() (in module prism.deconvolute) means_ (prism.mixture.BetaBinomialMixture attribute) merge_met_files() (in module prism.deconvolute)

merge_subclones() (in module prism.deconvolute) merge_two_headers() (in module prism.util) methylated_pattern() (in module prism.deconvolute)

O

overlaps() (in module prism.deconvolute)

P

param_generator() (in module prism.preprocess) parse_cn_line() (in module prism.deconvolute) parse_met_file() (in module prism.deconvolute) parse_result_line() (in module prism.util) pattern_counters_from_met() (in module prism.util) postfiltered() (in module prism.deconvolute) posthoc_process() (in module prism.deconvolute) predict_proba() (prism.mixture.BetaBinomialMixture method) prefiltered() (in module prism.preprocess) prepare_header_bed() (in module prism.util) preset_rc() (in module prism.util)

prism.annotate (module) prism.deconvolute (module) prism.extract (module) prism.hmm (module) prism.mixture (module) prism.preprocess (module) prism.proofreading (module) prism.scatter (module) prism.util (module) proba() (prism.hmm.HMMModel method) proofread() (in module prism.proofreading) proofread_given_n_template() (in module prism.proofreading)

R

random_pattern() (in module prism.util) Region (class in prism.util) run() (in module prism.annotate) (in module prism.deconvolute) (in module prism.extract) (in module prism.preprocess) (in module prism.scatter)

S

save_met_file() (in module prism.extract) scatter_1d() (in module prism.annotate) (in module prism.scatter)

scatter_2d() (in module prism.annotate) (in module prism.scatter)

T

trigamma() (in module prism.mixture)