trigger-trait: Trait-trigger analysis

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

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

  ## S4 method for signature 'trigger'
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

A vector of p-values associated with each tested causal regulator.

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.

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

See Also

trigger.loclink and trigger.export2cross

Examples

 ## 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)

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