trigger.net-methods {trigger} | R Documentation

## Network-Trigger analysis

### Description

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.

### Usage

      	## 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)

### Arguments

`triggerobj` | An object of class `trigger` containing slot `loc.obj` with local-linkage probabilities and marker indices of the best local-linkage markers for genes in the genome. See `trigger` and `trigger.loclink` for details.
`gender` | Optional. When computing statistics involving markers on sex chromosome, `gender` of each sample should be specified.
`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 `prob.cut = 0.7`.
`include.loc` | Logical. If `TRUE`, the estimated posterior probability of regulation is more conservative.
`seed` | Optional. A numeric seed for reproducible results.
`inputfile` | Optional. If provided, reads in the probability matrix from working directory.

### Details

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.

### Value

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.

### Author(s)

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

### References

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.

### See Also

`trigger.loclink`, `trigger.netPlot2ps` and `trigger.trait`

### Examples

     ## 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)

[Package trigger version 1.26.0 Index]