indexFinder: Finds the indices, in the model fields, of the species that...

In saezlab/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Finds the indices, in the model fields, of the species that are measured/inhibited/stimulated

Description

This function finds the indices, in the model fields, of the species that are measured/inhibited/stimulated. It looks for their position in model$namesSpecies which has the same order as the rows of interMat and notMat, and therefore these indexes can be used there as well.

Usage

indexFinder(CNOlist, model,verbose=FALSE)

Arguments

CNOlist	a CNOlist structure, as produced by makeCNOlist
model	a model structure, as produced by readSIF
verbose	do you want information about the cues and signals identities printed on the screen? Default if false but we would advise to set it to true when the function is called for the first time.

Value

a list with fields:

signals	vector of indices of the measured species
stimulated	vector of indices of the stimulated species
inhibited	vector of indices of the inhibited species

Note

For internal usage since version 1.3.28

Author(s)

C. Terfve

See Also

makeCNOlist, readSIF

Examples

data(CNOlistToy,package="CellNOptR")
data(ToyModel,package="CellNOptR")
indicesToy<-indexFinder(CNOlistToy,ToyModel,verbose=TRUE)

saezlab/CellNOptR documentation built on April 16, 2024, 5:21 a.m.