Description Usage Arguments Details Value Author(s) References See Also Examples

Network-Trigger analysis estimates the joint posterior probability of causal regulation for each pair of genes in the genome. These probabilities can further be used to construct a gene regulatory network.

1 2 3 | ```
## S4 method for signature 'trigger'
trigger.net(triggerobj, gender = NULL, idx = NULL,
Bsec = 100, prob.cut = 0.7, include.loc = TRUE, seed = 123, inputfile = NULL)
``` |

`triggerobj` |
An object of class |

`gender` |
Optional. When computing statistics involving markers on sex chromosome, |

`idx` |
Optional. One can specify the indices of selected genes as putative regulators. By default, all the genes will be selected as putative regulators. |

`Bsec` |
Number of iterations to perform when estimating null statistics for secondary-linkage and conditional independence. |

`prob.cut` |
Probability threshold. The joint regulatory probabilities of a regulator to all the other genes will be set to zero if the local-linkage probability of the regulator is below the threshold; default |

`include.loc` |
Logical. If |

`seed` |
Optional. A numeric seed for reproducible results. |

`inputfile` |
Optional. If provided, reads in the probability matrix from working directory. |

The option `idx`

contains the indices of putative regulator genes. When the data set is large, one can use this option by selecting a subset of genes as putative regulators in one computation and parallel-computes the genome-wide regulatory probability. If `idx=NULL`

, all the genes will be computed for probability of regulation to other genes in the data.

If `include.loc = TRUE`

, the joint posterior probability of regulation is the product of local-linkage, secondary-linkage and conditional independence. Otherwise, it is the product of secondary-linkage and conditional independence. The local-linkage is not a necessary condition for calculating regulation probability. If the probability of local-linkage is considered, the joint probability of regulation is more conservative. See references for details.

A matrix of genome-wide regulatory probabilities with putative regulators in rows and regulated genes in columns. Note that the matrix is not symmetric. If gene i is estimated to be causal for gene j with high probability, the reverse is not true.

Lin S. Chen lschen.stat@gmail.com, Dipen P. Sangurdekar dps@genomics.princeton.edu and John D. Storey jstorey@princeton.edu

Chen L.S., Emmert-Streib F., and Storey J.D. (2007) Harnessing naturally randomized transcription to infer regulatory relationships among genes. *Genome Biology*, **8:** R219.

`trigger.loclink`

, `trigger.netPlot2ps`

and `trigger.trait`

1 2 3 4 5 6 7 8 9 10 11 | ```
## Not run:
data(yeast)
attach(yeast)
triggerobj <- trigger.build(marker = marker, exp = exp,
marker.pos = marker.pos, exp.pos = exp.pos)
triggerobj <- nettrig.loc(triggerobj, window.size = 30000)
trig.prob <- trigger.net(triggerobj, Bsec = 100)
netPlot2ps(trig.prob)
detach(yeast)
## End(Not run)
``` |

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