lineage.import_lineage

This file includes functions to import the new lineage data.

Functions

import_AU565(path)

Importing AU565 file cells.

assign_observs_AU565(cell, lineage, uniq_id)

Given a cell, the lineage, and the unique id of the cell, it assigns the observations of that cell, and returns it.

import_MCF10A(path)

Reading the data and extracting lineages and assigning their corresponding observations.

assign_observs_MCF10A(cell, lineage, uniq_id)

Given a cell, the lineage, and the unique id of the cell, it assigns the observations of that cell, and returns it.

MCF10A(condition)

Creates the population of lineages for each condition.

Module Contents

lineage.import_lineage.import_AU565(path)

Importing AU565 file cells. :param path: the path to the file. :return population: list of cells structured in CellVar objects.

Parameters:

path (str)

Return type:

list

lineage.import_lineage.assign_observs_AU565(cell, lineage, uniq_id)

Given a cell, the lineage, and the unique id of the cell, it assigns the observations of that cell, and returns it. :param cell: a CellVar object to be assigned observations. :param lineage: the lineage list of cells that the given cell is from. :param uniq_id: the id given to the cell from the experiment.

Parameters:
Return type:

lineage.CellVar.CellVar

lineage.import_lineage.import_MCF10A(path)

Reading the data and extracting lineages and assigning their corresponding observations. :param path: the path to the mcf10a data. :return population: list of cells structured in CellVar objects.

Parameters:

path (str)

Return type:

list[list[lineage.CellVar.CellVar]]

lineage.import_lineage.assign_observs_MCF10A(cell, lineage, uniq_id)

Given a cell, the lineage, and the unique id of the cell, it assigns the observations of that cell, and returns it. :param cell: a CellVar object to be assigned observations. :param lineage: the lineage list of cells that the given cell is from. :param uniq_id: the id given to the cell from the experiment.

Parameters:
Return type:

lineage.CellVar.CellVar

lineage.import_lineage.MCF10A(condition)

Creates the population of lineages for each condition. Conditions include: PBS, EGF-treated, HGF-treated, OSM-treated. :param condition: a condition between [PBS, EGF, HGF, OSM]

Parameters:

condition (str)

Return type:

list[list]