sismonr (version 2.1.0)

getGRN: Returns an igraph object (network) of the GRN of the in silico system.

Description

Returns an igraph object (network) corresponding to the gene regulatory network of the insilico system, including all types of regulation of only those defined by the user.

Usage

getGRN(insilicosystem, edgeType = NULL, showAllVertices = F)

Arguments

insilicosystem

The in silico system (see createInSilicoSystem).

edgeType

The type of interactions to include in the network. If NULL (default value), all the interactions are included. Otherwise, can be either:

• "TC": return only regulation of transcription

• "TL": return only regulation of translation

• "RD": return only regulation of RNA decay

• "PD": return only regulation of protein decay

• "PTM": return only regulation of protein post-translational modification

• "RegComplexes": return only binding interactions, i.e. linking the regulatory complexes to their components.

showAllVertices

Display vertices that don't have any edge? Default is FALSE.

Examples

# NOT RUN {
mysystem = createInSilicoSystem(G = 10)
grn = getGRN(mysystem)
grnTC = getGRN(mysystem, edgeType = "TC", showAllVertices = F)
grnTCall = getGRN(mysystem, edgeType = "TC", showAllVertices = T)
# }