sismonr (version 2.1.0)

createRegulatoryNetwork: Creates an in silico regulatory network.

Description

Creates an in silico regulatory network given a list of regulators and targets.

Usage

createRegulatoryNetwork(
  regsList,
  tarsList,
  reaction,
  sysargs,
  ev = getJuliaEvaluator()
)

Arguments

regsList

A named list of length 2. Element "PC" (resp."NC") is a vector of gene IDs of the protein-coding (resp. noncoding) regulators for the network.

tarsList

A named list of length 2. Element "PC" (resp."NC") is a vector of gene IDs of the potential targets of the protein-coding (resp. noncoding) regulators.

reaction

String. The ID of the reaction targeted by the interactions ("TC", "TL", "RD", "PD" or "PTM").

sysargs

An object of class insilicosystemargs (i.e. a list with parameters for in silico system generation).

ev

A Julia evaluator (for the XRJulia package). If none provided select the current evaluator or create one if no evaluator exists.

Value

A list of two elements:

• edg: a data-frame of edges of the network with the following variables:

  • from: gene ID of the regulator, as a character;

  • to: gene ID of the target, as an integer;

  • TargetReaction: the ID of the reaction (as given by reaction);

  • RegSign: The sign of the reaction ("1" or "-1");

  • RegBy: Is the regulator a protein-coding gene ("PC"), a noncoding gene ("NC") or a complex ("C")?

• complexes: a list of complexes composition (each element is named with the complex ID, the components are given as gene IDs).

• complexesTargetReaction: a list defining which expression step the different regulatory complexes target (each element is named with the complex ID, the targeted reaction are given with a reaction ID, e.g. "TC" for transcription).

Examples

# NOT RUN {
## We want to create a small transcription regulatory network
## In this example, genes 1 and 2 are protein-coding regulators (say transcription factors),
## gene 3 is a noncoding regulator (say an miRNA), and genes 4-6 are the genes to be regulated
## (all protein-coding, e.g. all encoding enzymes)
createRegulatoryNetwork(regsList = list("PC" = c(1:2), "NC" = c(3)),
     tarsList = list("PC" = c(4:6), "NC" = integer(0)), reaction = "TC",
     sysargs = insilicosystemargs(G = 6))
# }