trigger.mlink-methods {trigger} | R Documentation

## Multi-Locus Linkage (Epistasis) Analysis

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

### 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)

[Package trigger version 1.38.0 Index]