View source: R/in_silico_system.R
createInSilicoSystem | R Documentation |
Creates an in silico system, i.e. the genes and the regulatory network defining the system.
createInSilicoSystem(empty = F, ev = getJuliaEvaluator(), ...)
empty |
Logical. Does the regulatory network is empty (= no regulation)? Default value is |
ev |
A Julia evaluator (for the XRJulia package). If none provided select the current evaluator or create one if no evaluator exists. |
... |
Other arguments to be passed to the function |
An object of class insilicosystem
, that is a list composed of:
genes
: a data-frame of genes (see createGenes
);
edg
: a data-frame of edges in the regulatory network (see createMultiOmicNetwork
);
mosystem
: a list defining the regulatory network (see createMultiOmicNetwork
);
sysargs
: An object of class insilicosystemargs
; the parameters used to create the system.
## Not run: ## Creates an in silico system composed of 20 genes mysystem1 = createInSilicoSystem(G = 20) mysystem1$edg ## see all regulations in the system mysystem1$mosystem$TCRN_edg ## see only regulations targeting transcription ## Creates an in silico systerm composed of 10 genes, all protein-coding mysystem2 = createInSilicoSystem(G = 10, PC.p = 1) mysystem2$genes ## Creates an in silico systerm composed of 5 genes, ## all noncoding and all regulators of transcription mysystem3 = createInSilicoSystem(G = 5, PC.p = 0, NC.TC.p = 1) mysystem3$edg mysystem3$mosystem$TCRN_edg ## End(Not run)
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