View source: R/in_silico_system.R
createRegulatoryNetwork | R Documentation |
Creates an in silico regulatory network given a list of regulators and targets.
createRegulatoryNetwork( regsList, tarsList, reaction, sysargs, ev = getJuliaEvaluator() )
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 |
ev |
A Julia evaluator (for the XRJulia package). If none provided select the current evaluator or create one if no evaluator exists. |
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).
## 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)) ## End(Not run)
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