R: Get state transitions between a state and its attractor

getPathToAttractor {BoolNet} | R Documentation

## 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

    # 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)

[Package BoolNet version 2.1.4 Index]