Description Usage Arguments Value Examples
View source: R/in_silico_system.R
Creates an in silico system, i.e. the genes and the regulatory network defining the system.
1 | 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## 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
|
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