Creates an empty in silico system (i.e. no regulatory interactions) given a data-frame of genes (cf
A data-frame of the genes existing in the system (see
An in silico system, that is a list of:
genes: the modified data-frame of genes;
edg: A data-frame of edges in the regulatory network of the system (1 row = 1 edge, here empty dataframe). It contains the following parameters:
from: gene ID of the edge origin (character).
to: gene ID of edge destination (character).
TargetReaction: Type of regulation (ID of the controlled reaction: "TC", "TL", "RD", "PD" or "PTM").
RegSign: Sign of the reaction ("1" for positive regulation, "-1" for negative regulation).
RegBy: Type of the regulator: "PC" for protein-coding regulation, "NC" for noncoding regulator,
"C" for regulatory complex.
mosystem: A list of the different regulatory networks (each corresponding to a different type of regulation) in the system and associated information. Elements of the list are
PTMRN_edg: data-frames of edges for the different
regulatory networks, which in addition to the usual fields in the
edg data frame, contain columns for kinetic parameters of the
regulation. All empty.
complexes: a list of regulatory complexes composition. The names of the elements are the IDs of the complexes, and the
values are vectors of gene IDs constituting each regulatory complex. Empty list.
complexeskinetics: a list of regulatory complexes kinetic parameters. Empty list.
complexesTargetReaction: a list defining which expression step is targeted by each regulatory complex.
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