trigger.trait-methods {trigger} | R Documentation |
Trait-Trigger identifies, for a given trait of interest, causal gene regulator(s) that makes the trait conditionally independent of the QTL and their estimated p-values of causal regulation. These probabilities can further be used to construct a gene regulatory network.
## S4 method for signature 'trigger' trigger.trait(triggerobj, trait, cross, thr, n.sv = NULL, addplot = TRUE)
triggerobj |
|
trait |
Trait for which causal regulator is to be found. It can either be a gene-name for a gene expression trait present in |
cross |
An object of class |
thr |
LOD threshold to search for locally linked putative causal genes (default 3). |
n.sv |
Number of surrogate variables used to model the local heterogeneity. If not set, it is computed from the expression data. |
addplot |
If |
A vector of p-values associated with each tested causal regulator.
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.
Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889–890.
trigger.loclink
and trigger.export2cross
## Not run: data(yeast) attach(yeast) triggerobj <- trigger.build(marker = marker, exp = exp, marker.pos = marker.pos, exp.pos = exp.pos) crossfile <- trigger.export2cross(triggerobj) tt.pval <- trigger.trait(triggerobj, trait = "DSE1", cross = crossfile) causal.reg <- names(which(p.adjust(tt.pval, method = "fdr")<.05)) detach(yeast) ## End(Not run)