plot {trigger} | R Documentation

## Graphical Display of Trigger Analysis

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

### 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)

[Package trigger version 1.40.0 Index]