CNOlist-methods: List of CNOlist-class methods

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

Description

CNOlist is a class with a set of methods described here below.

Usage

signature(x="CNOlist")

Getters

getCues

Returns the cues (matrix) found in the CNOlist

getSignals

Returns the signals (list of matrices) found in the CNOlist

getStimuli

Returns the cues found in the CNOlist

getInhibitors

Returns the inhibitors found in the CNOlist

getTimepoints

Returns the timepoints found in the CNOlist

getVariances

Returns the Variances (list of matrices) found in the CNOlist. Will be different from zero only if replicates were found in the MIDAS data. See makeCNOlist

Setters

setSignals

Set the signals. No sanity check!

Other methods

compatCNOlist

convert the instance CNOlist into the old-style returned by makeCNOlist that is a list. Used in the ODE package.

length

returns length of CNOlist (number of time points)

randomize

randomizes the signals matrice in a CNOlist. See randomizeCNOlist for details

show

prints summary information

plot

plot the CNOlist instance using the plotCNOlist function.

plot

signature(x="CNOlist", y="CNOlist"): Please see the page of plotCNOlist2 for more details.

readErrors

signature(object="CNOlist", filename="MIDAS-file"): reads measurement error corresponding to the data from the MIDAS file and updates the CNOlist object

writeErrors

signature(object="CNOlist", filename="string",overwrite=F): writes measurement error corresponding to the data from the CNOlist to a MIDAS file

Author(s)

T.Cokelaer

See Also

CNOlist-class, randomizeCNOlist makeCNOlist

Examples

showClass("CNOlist")

data(CNOlistToyMMB, package="CellNOptR")
cnolist = CNOlistToyMMB

# In version 1.3.30 and above, use the plot method instead of former plotCNOlist function.
plot(cnolist)
# In version 1.5.14 and above, use getters instead of the @ operator
getCues(cnolist)

# others:
new_cnolist = randomize(cnolist)

CellNOptR documentation built on Nov. 8, 2020, 6:58 p.m.