getBasinOfAttraction: Get states in basin of attraction

In BoolNet: Construction, Simulation and Analysis of Boolean Networks

Get states in basin of attraction

Description

Extracts information on all states in the basin of a supplied attractor

Usage

getBasinOfAttraction(attractorInfo, attractorNo)

Arguments

attractorInfo	An object of class AttractorInfo, as returned by getAttractors, or of class SymbolicSimulation, as returned by simulateSymbolicModel. As the transition table information in this structure is required, getAttractors must be called in synchronous mode and with returnTable set to TRUE. Similarly, simulateSymbolicModel must be called with returnGraph=TRUE.
attractorNo	The index of the attractor in attractorInfo whose basin should be identified

Details

The function outputs a transition table containing only the states that are contained in the basin of attraction, and displays additional information on these states. If attractorInfo is the result of an exhaustive synchronous attractor search, the complete basin of attraction is returned. If attractorInfo is the result of a heuristic synchronous search, there is no guarantee that the complete basin of attraction is returned, as only the calculated states are included. Asynchronous search results are not supported, as no transition table is calculated.

Value

Returns a generic dataframe of the class TransitionTable. For n genes, the first n columns code for the original state, i.e. each column represents the value of one gene. The next n columns code for the successive state after a transition. The column attractorAssignment indicates the attractor to the state is assigned (in this case, attractorNo). If this information is available, the column stepsToAttractor indicates how many transitions are needed from the original state to the attractor. The TransitionTable class supports pretty printing using the print method.

See Also

getStateSummary, getTransitionTable, getAttractors, simulateSymbolicModel

Examples

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

# get attractors
attractors <- getAttractors(cellcycle)

# print basin of first attractor
print(getBasinOfAttraction(attractors, 1))

## End(Not run)

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