epistasis.matrix module¶
-
epistasis.matrix.
encode_vectors
(binary_genotypes, model_type='global')¶ Encode a set of binary genotypes is input vectors for the given model
-
epistasis.matrix.
get_model_matrix
(binary_genotypes, sites, model_type='global')¶ Get a model matrix for a given set of genotypes and coefficients.
Parameters: - binary_genotypes (list or array) – List of genotypes in their binary representation (see gpmap.utils.genotypes_to_binary)
- sites (list) – List of epistatic interaction sites.
- model_type (string) – Type of epistasis model (global/Hadamard, local/Biochemical).
-
epistasis.matrix.
get_pandas_matrix
(binary_genotypes, sites, matrix=None, model_type='global')¶ Get epistasis model matrix as a Pandas DataFrame.
This is useful for visualizing the matrix in a Jupyter Notebook.
Parameters: - binary_genotypes (list or array) – List of genotypes in their binary representation (see gpmap.utils.genotypes_to_binary)
- sites (list) – List of epistatic interaction sites.
- model_type (string) – Type of epistasis model (global/Hadamard, local/Biochemical).