sismonr (version 2.1.0)

createInSilicoSystem: Creates an in silico system.

Description

Creates an in silico system, i.e. the genes and the regulatory network defining the system.

Usage

createInSilicoSystem(empty = F, ev = getJuliaEvaluator(), ...)

Arguments

empty

Logical. Does the regulatory network is empty (= no regulation)? Default value is FALSE.

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 insilicosystemargs (i.e. parameters for the generation of the in silico system).

Value

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.

Examples

# 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
# }