trigger-mlink: Multi-Locus Linkage (Epistasis) Analysis

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

Description

Multi-locus linkage (epistasis) analysis.

Usage

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

Arguments

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.

Details

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).

Value

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.

Author(s)

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

References

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.

See Also

trigger.link and plot

Examples

## 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)

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