trigger.loclink-methods {trigger} | R Documentation

## Estimate local-linkage probability for each gene

### Description

A method of class `trigger` to identify the best local-linkage marker for each gene and compute the local linkage probabilities.

### Usage

     	## S4 method for signature 'trigger'
    trigger.loclink(triggerobj, gender = NULL, window.size = 30000)

### Arguments

`triggerobj` | An object of class `trigger`.
`gender` | Optional. When computing linkage statistics involving markers on sex chromosome, `gender` of each sample should be specified.
`window.size` | Optional. The size of a window that places the putative regulator gene in the center. Every marker within the window is a candidate marker for local-linkage to the regulator gene.

### Value

An updated object of class `trigger` containing a slot `loc.obj` with fields:

`prob.loc` | The estimated local-linkage probability for each putative regulator gene.
`loc.idx` | The indices of the best local marker for each putative regulator gene.

Use `slot(triggerobj, "loc.obj")` to retrieve the list.

### 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.trait`

### Examples

    ## Not run:
      data(yeast)
      attach(yeast)
      triggerobj <- trigger.build(marker = marker, exp = exp,
                marker.pos = marker.pos, exp.pos = exp.pos)
      triggerobj <- trigger.loclink(triggerobj, window.size = 30000)
      trigger.obj <- trigger.net(triggerobj, Bsec = 100)
      detach(yeast)

    ## End(Not run)

[Package trigger version 1.32.0 Index]