Preprocessing (pasmopy.preprocessing)

class pasmopy.preprocessing.weighting_factors.WeightingFactors(model, gene_expression)

Prepare for adding information about gene expression data to model.

model

BioMASS model object.

Type:

biomass.model_object.ModelObject

gene_expression

Pairs of proteins and their related genes.

Type:

dict

weighting_factors

List of weighting factors.

Type:

list of strings

prefix

Prefix of weighting factors on gene expression levels.

Type:

str (default: “w_”)

indentation

How many spaces as indentation.

Type:

str (default: 4 spaces)

Examples

>>> import erbb_network
>>> model = Model(erbb_network.__package__).create()
>>> gene_expression = {
...     "ErbB1": ["EGFR"],
...     "ErbB2": ["ERBB2"],
...     "ErbB3": ["ERBB3"],
...     "ErbB4": ["ERBB4"],
...     "Grb2": ["GRB2"],
...     "Shc": ["SHC1", "SHC2", "SHC3", "SHC4"],
...     "RasGAP": ["RASA1", "RASA2", "RASA3"],
...     "PI3K": ["PIK3CA", "PIK3CB", "PIK3CD", "PIK3CG"],
...     "PTEN": ["PTEN"],
...     "SOS": ["SOS1", "SOS2"],
...     "Gab1": ["GAB1"],
...     "RasGDP": ["HRAS", "KRAS", "NRAS"],
...     "Raf": ["ARAF", "BRAF", "RAF1"],
...     "MEK": ["MAP2K1", "MAP2K2"],
...     "ERK": ["MAPK1", "MAPK3"],
...     "Akt": ["AKT1", "AKT2"],
...     "PTP1B": ["PTPN1"],
...     "GSK3b": ["GSK3B"],
...     "DUSP": ["DUSP5", "DUSP6", "DUSP7"],
...     "cMyc": ["MYC"],
... }
>>> weighting_factors = WeightingFactors(model, gene_expression)
>>> weighting_factors.add_to_params()
>>> weighting_factors.set_search_bounds()

add_to_params()

Add weighting factors to model parameters.

Return type:

None

set_search_bounds(lb=0.01, ub=100.0)

Set search bounds for weighting factors.

Parameters:

• lb (float (default: 0.01)) – Lower bound.

• ub (float (default: 100.0)) – Upper bound.

Return type:

None