pygot.tools.analysis.GRNData#

class pygot.tools.analysis.GRNData(G_hat: GeneRegulatroyModel, beta_hat: GeneDegradation, tf_names, gene_names)[source]#

Bases: object

Gene regulatory network data structure

This class store the variable of infered grn

Variable:#

self.G: np.ndarray, (n_gene, n_tf): Regulatory strength, self.G[i,j] represent the regulatory strength of gene j to gene i
self.beta: np.ndarray (n_gene,): Degrade rate of genes
self.ranked_edges: pd.DataFrame: Ranked regulatory relationship
self.tf_names: list: TF names
self.gene_names: list: Gene names
self.models: dict: self.models[‘G’] is torch model of G, self.models[‘beta’] is torch model of beta

__init__(G_hat: GeneRegulatroyModel, beta_hat: GeneDegradation, tf_names, gene_names)[source]#

initial function

Methods

`__init__`(G_hat, beta_hat, tf_names, gene_names)	initial function
`export_grn_into_celloracle`(oracle)	CellOracle interface

export_grn_into_celloracle(oracle)[source]#

CellOracle interface

Export the fitted GRN into CellOracle for further analysis, such as perturbation