Description Usage Arguments Details Examples
A function that takes a set of perturbation rules as input and creates a perturbation matrix to be used for modular response analysis.
1 | read.rules(obj)
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obj |
Either the path to a perturbation rules file without header or a vector of strings specifying the perturbation rules (see details). |
Perturbations rules are a set of strings specifying the action of perturbations upon modules in a network. In both cases modules and perturbations must have the same names as the names of rows and columns in experimental data tables (names are case sensitive).
The rules syntax must be “'Perturbation->Module“' for a single perturbation,“'Perturbation->0“' to specify the basal line and “'0->Module“' to specify modules that were not perturbated but for which connectivity coming from other modules can be retrieved. At least two rules and a basal line must be written.
1 2 | rules=c("Et->Luciferase","E2+siRIP140->RIP140","E2+siLCoR->LCoR","E2->0")
read.rules(rules)
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