Description Usage Arguments Value Examples
View source: R/in_silico_system.R
Creates an in silico regulatory network given a list of regulators and targets.
1 2 3 4 5 6 7 | 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).
1 2 3 4 5 6 7 | ## 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))
|
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