plot: Graphical Display of Trigger Analysis

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

Description

Graphical display of genomewide linkage map, multi-locus linkage or eQTL variation

Usage

	## S4 method for signature 'trigger,missing'
plot(x,y,type = c("link", "mlink", "eqtl"),
				cutoff  = 3.3e-4, qcut = 0.1, bin.size = NULL)

Arguments

x	An object of class trigger.
y	Ignore option, not used.
type	An argument describing the type of plot. Select from link (default) for genome-wide linkage map, eqtl.R2 for graphical display of eQTL-R^2 contribution or mlink for display of genome-wide epistasis effect.
cutoff	Threshold value for link. The measures below the threshold are called significant and are plotted.
qcut	Q-value threshold for mlink. The joint multi-locus linkage probabilities with q-values below the threshold are called significant and are plotted.
bin.size	Optional for mlink. If not NULL, each chromosome will be divided into several bins, each with size bin.size. Markers within a bin will be considered as at a same position.

Author(s)

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

See Also

trigger.link, trigger.mlink and trigger.eigenR2

Examples

 ## Not run: 
  
  data(yeast)
  attach(yeast)
  triggerobj <- trigger.build(marker=marker, exp=exp, 
				marker.pos=marker.pos, exp.pos=exp.pos)
  triggerobj <- trigger.link(triggerobj, gender=NULL, norm=TRUE)
  plot(triggerobj,type = "link", cutoff=1e-5)
  triggerobj <- trigger.eigenR2(triggerobj, adjust=FALSE)
  plot(triggerobj, type = "eigenR2")
  triggerobj<- trigger.mlink(triggerobj, B=5, seed=123)
  plot(triggerobj, qcut=0.1, bin.size=NULL)
  
  detach(yeast)


## End(Not run)

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