getPathToAttractor: Get state transitions between a state and its attractor

In BoolNet: Construction, Simulation and Analysis of Boolean Networks

Get state transitions between a state and its attractor

Description

Lists the states in the path from a specified state to the corresponding synchronous attractor.

Usage

getPathToAttractor(network, 
                   state,
                   includeAttractorStates = c("all","first","none"))

Arguments

network	Either a network structure of class BooleanNetwork or SymbolicBooleanNetwork , or an attractor search result of class AttractorInfo. In the former case, a synchronous attractor search starting from state is conducted. In the latter case, network must be the result of a call to getAttractors with returnTable=TRUE, and its transition table must include state.
state	A binary vector with exactly one entry per gene in the network. If network is of class SymbolicBooleanNetwork and makes use of more than one predecessor state, this can also be a matrix with the genes in the columns and multiple predecessor states in the rows.
includeAttractorStates	Specifies whether the actual attractor states are included in the resulting table or not. If includeAttractorStates = "all" (which is the default behaviour), the sequence ends when the attractor was traversed once. If includeAttractorStates = "first", only the first state of attractor is added to the sequence. This corresponds to the behaviour prior to BoolNet version 1.5. If includeAttractorStates = "none", the sequence ends with the last non-attractor state. In this case, the sequence can be empty if the start state is an attractor state.

Value

Returns a data frame with the genes in the columns. The rows are the successive states from state to the the corresponding attractor. Depending on includeAttractorStates, attractor states are included or not. The data frame has an attribute attractor specifying the indices of the states that belong to the attractor. If includeAttractorStates is "first" or "none", these indices may correspond to states that are not included in the sequence itself. This attribute is used by plotSequence to highlight the attractor states.

See Also

getAttractors, simulateSymbolicModel, getTransitionTable, getBasinOfAttraction, plotSequence, attributes

Examples

## Not run: 
# load example network
data(cellcycle)

# get path from a state to its attractor
# include all attractor states
path <- getPathToAttractor(cellcycle, rep(1,10), 
                           includeAttractorStates="all")
print(path)

# include only the first attractor state
path <- getPathToAttractor(cellcycle, rep(1,10), 
                           includeAttractorStates="first")
print(path)

# exclude attractor states
path <- getPathToAttractor(cellcycle, rep(1,10), 
                           includeAttractorStates="none")
print(path)

## End(Not run)

BoolNet documentation built on Oct. 2, 2023, 5:08 p.m.