pyscnet.Preprocessing

pyscnet.Preprocessing.gnetdata

Created on Wed May 22 13:53:34 2019

@author: mwu

class pyscnet.Preprocessing.gnetdata.Gnetdata(Exp, CellAttrs=None, GeneAttrs=None)

Bases: object

Gnetdata class includes dataset specifically

for building GRNs. It consists four sub-classes: 1) Exp: A dict of sparse matrix, var_names and obj_names 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 Exp and the keys of CellAttrs, GeneAttrs, NetAttrs

save_as(outpath)

save as pickle object

property shape

return the shape of Exp

pyscnet.Preprocessing.gnetdata.load_Gnetdata_object(filepath)

load Gnetdata (pickle) from local

param filepath:

str, default None.

return:

Gnetdata

pyscnet.Preprocessing.gnetdata.load_from_anndata(anndata_obj=None)

Load adata object

param anndata_obj:

adata object, default None

return:

Gnetdata