Get_all_attractors.f: Get attractors of a Boolean model

In SPIDDOR/SPIDDOR: SPIDDOR

Description

Identifies the attractors of a Boolean model using the synchronous or asynchronous updating methods.

Usage

Get_all_attractors.f(cpus,BN,asynchronous=FALSE,repetitions=0,
                     startStates=NULL,Percent.ON=TRUE)

Arguments

cpus	Number of cpus requested for the cluster in order to parallelize the code
BN	A list containing the most relevant information of the loaded network. See read.Boolean.functions for more details.
asynchronous	logical; if FALSE the synchronous mode is selected; if TRUE the asynchronous scheme is chosen (by default).
repetitions	Number of repetitions to re-compute the simulation algorithm in order to get the attractors in the asynchronous mode. We recommend first to try with a number smaller that 20. More than 60 repetitions are not allowed.
startStates	A number of starting states to test. No more than 1,000,000 starting states are not allowed.
Percent.ON	logical. If TRUE returns the attractor represented as the probability of activation of the nodes in the network. If FALSE returns all the states that form the attractor. Default is TRUE. If this function is used with asynchronous=TRUE, the results only will be returned with the nodes represented as %ON.

Details

The function searches all the attractors for networks with less than 20 nodes, as the number of initial conditions to test grow exponentially with the number of nodes. For larger networks, a subset of nodes can be defined in BN$Initial_conditions vector (<20 node names) in which all the combination of initial conditions will be tested. Additionally, a number of starting states to test can be specified in the startStates argument of the function (<1,000,000).

This function is parallelized with the snowfall library.

Value

A data frame with all the attractors represented with the probability of activation of each node, and the recurrence of each attractor.

References

Saadatpour A, Albert I, Albert R (2010). Attractor analysis of asynchronous Boolean models of signal transduction networks. J Theor Biol.

Examples

## Not run: 
#Load the data:
data("cellcycle")
BN_cellcycle<-read.Boolean.functions(Lines=BN_cellcycle$BooleanFunctions)

#Get all the synchronous attractors:
All_attr_syn<-Get_all_attractors.f(cpus=4,BN_cellcycle,asynchronous=FALSE,Percent.ON=FALSE)
print(All_attr_syn)

## End(Not run)

SPIDDOR/SPIDDOR documentation built on May 9, 2019, 11:42 a.m.