prism.hmm module¶

class prism.hmm.HMMModel(template_pattern, e_m=0.01, e_d=0.001, e_b=0.01, p=0.96, q=0.96)[source]¶

DNMT1-like HMM model for in silico proofreading.

proba(seq)[source]¶

Returns the probability of the observed methylation pattern sequence given the template pattern.

Parameters:	seq (list) – Binary representation of methylation pattern sequence.
Returns:	Probability of the observed methylation pattern based on the model.

prism.hmm.is_methylated(base)[source]¶

Returns True if the base denotes methylated cytosine.

Parameters:	base (int) – Binary representation of methylation state of a cytosine.
Returns:	True if base == 1 else False