trigger.trait-methods: Trait-trigger analysis

Description

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.

Usage

"trigger.trait"(triggerobj, trait, cross, thr, n.sv = NULL, addplot = TRUE)

Arguments

triggerobj

An object of class trigger. See trigger for details.

trait

Trait for which causal regulator is to be found. It can either be a gene-name for a gene expression trait present in triggerobj or a vector of values for the individuals present in triggerobj.

cross

An object of class cross obtained from trigger.export2cross. See R/qtl for more details.

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 TRUE, a plot of the LOD scores from a genome-scan for a single-QTL model from package R/qtl.

Value

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.

Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889--890.

Examples

Run this code

 ## 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)