epistasis.simulate package¶
epistasis.simulate.base module¶
epistasis.simulate.linear module¶
-
class
epistasis.simulate.linear.
LinearSimulation
(wildtype, mutations, model_type='global', **kwargs)¶ Bases:
epistasis.simulate.base.BaseSimulation
Construct an genotype-phenotype from linear building blocks and epistatic coefficients.
Example
Phenotype = b0 + b1 + b2 + b3 + b12 + b13 + b13 + b123
Parameters: - wildtype (str) – Wildtype genotype
- mutations (dict) – Mapping for each site to its alphabet
- order (int) – Order of epistasis in simulated genotype-phenotype map
- betas (array-like) – values of epistatic coefficients (must be positive for this function to work. Log is taken)
- model_type (str) – Use a local or global (i.e. Walsh space) epistasis model to construct phenotypes
-
build
()¶ Build the phenotype map from epistatic interactions.