trigger.loclink-methods {trigger} | R Documentation |
A method of class trigger
to identify the best local-linkage marker for each gene and compute the local linkage probabilities.
## S4 method for signature 'trigger' trigger.loclink(triggerobj, gender = NULL, window.size = 30000)
triggerobj |
An object of class |
gender |
Optional. When computing linkage statistics involving markers on sex chromosome, |
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. |
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.
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.
## 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)