trigger-mlink: Multi-Locus Linkage (Epistasis) Analysis
In igbucur/trigger: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Description Usage Arguments Details Value Author(s) References See Also Examples

Multi-locus linkage (epistasis) analysis.

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  ## S4 method for signature 'trigger'
trigger.mlink(triggerobj, prob.cut = 0.9, 
	gender = NULL, idx = NULL, B = 5, seed = 123)

`triggerobj`	An object of class `trigger`.
`prob.cut`	Probability threshold for primary linkage.
`gender`	Optional. When computing linkage statistics involving markers on sex chromosome, `gender` of each sample should be specified.
`idx`	The indices for genes to be computed for multi-locus linkage.
`B`	The number of null iterations to perform.
`seed`	Optional. A numeric seed for reproducible results.

When data set is large, one can the option idx to select a subset of genes in each computation and parallel-computes the genome-wide multi-locus linkage. Since the function computes the linkage probability by borrowing information across genes, at least more than 100 genes should be selected in applying this function. If idx=NULL, all the genes in the input data will be computed for multi-locus linkage.

The current version of the function could only compute two-locus joint linkage (epistasis).

An updated object of class trigger containing a slot trigger.mlink with fields:

`qtl`	The major and secondary QTLs for each selected gene.
`prob`	The posterior probability of linkage for major QTL, secondary QTL, and the joint posterior probability of multi-locus linkage.
`qvalue`	Q-value estimates for joint multi-locus linkage probabilities.

Use slot(triggerobj, "mlink") to retrieve the list.

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

Brem R.B., Storey J.D., Whittle J., and Kruglyak L. (2005) Genetic interactions between polymorphisms that affect gene expression in yeast. Nature, 436(7051): 701–703.

Storey J.D., Akey J.M., and Kruglyak L. (2005) Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biology, 3(8): 1380–1390.

trigger.link and plot

## Not run: 
	data(yeast)
    attach(yeast)
	triggerobj <- trigger.build(marker = marker,exp = exp, 
            marker.pos = marker.pos, exp.pos = exp.pos)
	## Genome-wide multiple locus linkage analysis
	triggerobj <- trigger.mlink(triggerobj, B = 10, idx = NULL, seed = 123)
  
	plot(triggerobj, type = "trigger.mlink", qcut=0.1, bin.size=NULL)
	mlink = slot(triggerobj, "trigger.mlink")
	detach(yeast)

## End(Not run)