perturb: Perturb a set of node/edge groups.

In csclab/RMut: RMut: a collective framework for mutations analysis in network dynamics

Description

Perturb a set of node/edge groups in a network.

Usage

perturb(network, groupSet, mutateMethod = "rule flip")

Arguments

network	The network contains the node/edge groups
groupSet	The indexing number of node/edge groups in the network
mutateMethod	The method of mutation to be performed, default is "rule flip"

Details

This function perturbs a set of node/edge groups in a network. Two parameters groupSet, and mutateMethod have same meaning as in the calSensitivity function.

Value

None. Error messages or information would be outputed to the screen.

See Also

restore, generateGroups, generateGroup, calSensitivity, findAttractors

Examples

data(amrn)
# Generate a group of two nodes and two edges in the AMRN network
amrn <- generateGroup(amrn, nodes = "AG, SUP", edges = "UFO (1) PI, LUG (-1) PI")
print(amrn$Group_1)

# Generate a specific initial-state for the AMRN network
state1 <- generateState(amrn, "1110011011")

# Find the original transition network (before making perturbations)
transNet <- findAttractors(amrn, state1)
print(transNet)

# Perturb the group with overexpression mutation,
#  in this case only two nodes (AG, SUP) of the group are affected by the mutation.
perturb(amrn, 1, "overexpression")

# Continuously perturb the group with edge-removal mutation,
#  in this case only two edges of the group are removed by the mutation.
perturb(amrn, 1, "edge removal")

# Continuously perturb the group with "state-flip" mutation,
#  thus only two nodes (AG, SUP) of the group are affected by the mutation.
perturb(amrn, 1, "state flip")

# Find the perturbed transition network
perturbed_transNet <- findAttractors(amrn, state1)
print(perturbed_transNet)

csclab/RMut documentation built on May 14, 2019, 12:07 p.m.