inference,micro_array-method {Cascade} | R Documentation |

## Reverse-engineer the network

### Description

Reverse-engineer the network.

### Usage

```
## S4 method for signature 'micro_array'
inference(
M,
tour.max = 30,
g = function(x) {
1/x
},
conv = 0.001,
cv.subjects = TRUE,
nb.folds = NULL,
eps = 10^-5,
type.inf = "iterative"
)
```

### Arguments

`M` |
a micro_array object. |

`tour.max` |
maximal number of steps. Defaults to 'tour.max=30' |

`g` |
the new solution is choosen as (the old solution + g(x) * the new solution)/(1+g(x)) where x is the number of steps. Defaults to 'g=function(x) 1/x' |

`conv` |
convergence criterion. Defaults to 'conv=10e-3' |

`cv.subjects` |
should the cross validation be done removing the subject one by one ? Defaults to 'cv.subjects=TRUE'. |

`nb.folds` |
Relevant only if cv.subjects is FALSE. The number of folds in cross validation. Defaults to 'NULL'. |

`eps` |
machine zero. Defaults to '10e-5'. |

`type.inf` |
"iterative" or "noniterative" : should the algorithm be computed iteratively. Defaults to '"iterative"'. |

### Value

A network object.

### Author(s)

Nicolas Jung, Frédéric Bertrand , Myriam Maumy-Bertrand.

### References

Jung, N., Bertrand, F., Bahram, S., Vallat, L., and
Maumy-Bertrand, M. (2014). Cascade: a R-package to study, predict and
simulate the diffusion of a signal through a temporal gene network.
*Bioinformatics*, btt705.

Vallat, L., Kemper, C. A., Jung, N., Maumy-Bertrand, M., Bertrand, F.,
Meyer, N., ... & Bahram, S. (2013). Reverse-engineering the genetic
circuitry of a cancer cell with predicted intervention in chronic
lymphocytic leukemia. *Proceedings of the National Academy of
Sciences*, 110(2), 459-464.

### Examples

```
#With simulated data
data(M)
infM <- inference(M)
str(infM)
#With selection of genes from GSE39411
data(Selection)
infSel <- inference(Selection)
str(infSel)
```

*Cascade*version 2.1 Index]