trigger.trait-methods {trigger} | R Documentation

## Trait-trigger analysis

### Description

Trait-Trigger identifies, for a given trait of interest, causal gene regulator(s) that makes the trait conditionally independent of the QTL and their estimated p-values of causal regulation. These probabilities can further be used to construct a gene regulatory network.

### Usage

      ## S4 method for signature 'trigger'
    trigger.trait(triggerobj, trait, cross, thr, n.sv = NULL, addplot = TRUE)

### Arguments

`triggerobj` | An object of class `trigger`. See `trigger` for details.
`trait` | Trait for which causal regulator is to be found. It can either be a gene-name for a gene expression trait present in `triggerobj` or a vector of values for the individuals present in `triggerobj`.
`cross` | An object of class `cross` obtained from `trigger.export2cross`. See `R/qtl` for more details.
`thr` | LOD threshold to search for locally linked putative causal genes (default 3).
`n.sv` | Number of surrogate variables used to model the local heterogeneity. If not set, it is computed from the expression data.
`addplot` | If `TRUE`, a plot of the LOD scores from a genome-scan for a single-QTL model from package `R/qtl`.

### Value

A vector of p-values associated with each tested causal regulator.

### Author(s)

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

### References

Chen L.S., Emmert-Streib F., and Storey J.D. (2007) Harnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biology, 8: R219.

Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889–890.

### See Also

`trigger.loclink` and `trigger.export2cross`

### Examples

     ## Not run:
      data(yeast)
      attach(yeast)
      triggerobj <- trigger.build(marker = marker, exp = exp,
    				   marker.pos = marker.pos, exp.pos = exp.pos)
      crossfile <- trigger.export2cross(triggerobj)
      tt.pval <- trigger.trait(triggerobj, trait = "DSE1", cross = crossfile)
      causal.reg <- names(which(p.adjust(tt.pval, method = "fdr")<.05))
      detach(yeast)

    ## End(Not run)

[Package trigger version 1.28.0 Index]