trigger-loclink: Estimate local-linkage probability for each gene

In StoreyLab/trigger-devel: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

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 [e-mail], Dipen P. Sangurdekar [e-mail] and John D. Storey [e-mail]

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)

StoreyLab/trigger-devel documentation built on May 9, 2019, 3:11 p.m.