CNOlist-class: Class '"CNOlist"'

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

Class "CNOlist"

Description

This function takes as input the filename of a MIDAS file (or the list returned by makeCNOlist) and returns an instance of CNOlist class. It provides an object oriented approach to manipulate CNOlist. This function calls readMIDAS and makeCNOlist.

Objects from the Class

Objects can be created by calls of the form new("CNOlist", ...).

Slots

cues:

Object of class "matrix"

inhibitors:

Object of class "matrix"

stimuli:

Object of class "matrix"

signals:

Object of class "list"

variances:

Object of class "list"

timepoints:

Object of class "vector" timepoints contained in the signals matrix.

See CNOlist-methods for details

Methods

Available methods are plot, compatCNOlist, randomize, length. See CNOlist-methods for details.

Author(s)

T. Cokelaer

See Also

randomizeCNOlist, plotCNOlist, plotCNOlist2

Examples

showClass("CNOlist")

files<-dir(system.file("ToyModel",package="CellNOptR"),full=TRUE)
cnolist  = CNOlist(files[[1]])
# getters:
getCues(cnolist)
getInhibitors(cnolist)
getSignals(cnolist)
getVariances(cnolist)
getTimepoints(cnolist)
getStimuli(cnolist)
# In version 1.3.30 and above, use the plot method instead of former plotCNOlist function.
plot(cnolist)
new_cnolist = randomize(cnolist)
length(cnolist)

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