trigger-link: Genomewide eQTL analysis
In trigger: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Description Usage Arguments Value Author(s) See Also Examples

A method of class trigger for genomewide Expression-trait QTL analysis. This function estimates the linkage statistic and parametric p-value for each gene expression to every locus in the genome.

1 2	## S4 method for signature 'trigger' trigger.link(triggerobj, gender = NULL, norm = TRUE)

`triggerobj`	An object of class `trigger`.
`gender`	Optional. When computing linkage statistics involving markers on sex chromosome, `gender` of each sample should be specified.
`norm`	Logical. If `TRUE`, each row of expression matrix `exp` in the `triggerobj` will be transformed to follow a standard normal distribution, based on the rank of value.

An updated object of class trigger containing slots:

`stat`	A matrix of pair-wise likelihood ratio statistics for linkage analysis, with genes in rows and markers in columns.
`pvalue`	A matrix of parametric pvalues corresponding to statistics in the `stat` matrix.

Use slot(triggerobj, "stat") and slot(triggerobj, "pvalue") to retrieve the values.

Lin S. Chen lschen.stat@gmail.com, Dipen P. Sangurdekar dps@genomics.princeton.edu and John D. Storey jstorey@princeton.edu

plot and trigger.mlink

## 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)
  stat = slot(triggerobj, "stat"); pvalue = slot(triggerobj, "pvalue")
  detach(yeast)


## End(Not run)