pyscnet.Preprocessing

pyscnet.Preprocessing.gnetdata

Created on Wed May 22 13:53:34 2019

@author: mwu

class pyscnet.Preprocessing.gnetdata.Gnetdata(ExpMatrix, CellAttrs=None, GeneAttrs=None)[source]

Bases: object

for building GRNs. It consists four sub-classes: 1) ExpMatrix: A gene count matrix 2) CellAttrs: A dict gives information about cells. eg. cluster_nr, annotation 3) GeneAttrs: A dict gives information about genes. eg. module_nr, marker_annotation 4) NetAttrs: A dict includes Networks attributes. eg. node centralities.

property deepcopy

make a deepcopy of gnetData

property info

return the shape of ExpMatrix and the keys of CellAttrs, GeneAttrs, NetAttrs

save_as(outpath)[source]

save as pickle object

property shape

return the shape of ExpMatrix

pyscnet.Preprocessing.gnetdata.load_Gnetdata_object(filepath)[source]
Parameters

filepath – str, default None.

Returns

Gnetdata

pyscnet.Preprocessing.gnetdata.load_from_scanpy(scanpy_obj=None, filepath=None)[source]
Parameters
  • scanpy_obj – adata object, default None

  • filepath – str, default None. filepath refers to adata object

Returns

Gnetdata