trigger.export2cross-methods {trigger} | R Documentation

## Export Trigger data to R/qtl's cross class object

### Description

`trigger.export2cross` exports `trigger` data from `triggerobj` to a `cross` format for Trait-Trigger analysis. See `trigger.trait` for details.

### Usage

      ## S4 method for signature 'trigger'
    trigger.export2cross(triggerobj, plotarg = TRUE, verbose = TRUE, warning = FALSE)

### Arguments

`triggerobj` | An object of class `trigger`.
`plotarg` | Logical. If `TRUE`, the function plots the default plot from the `R/qtl` package while reading in the genotype data.
`verbose` | Logical. If `TRUE`, the function lists the default output from the `R/qtl` package while reading in the genotype data.
`warning` | Logical. If `FALSE`, the function suppresses warnings output from the `R/qtl` package while reading in the genotype data.

### Details

The `trigger.export2cross` command writes a `csv` format file “geno_trait_data.csv” to the working directory and reads it using the `read.cross` command.

### Value

An object of class cross from the `R/qtl` package.

### Author(s)

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

### References

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

### See Also

`trigger.trait`

### Examples

      data(yeast)
      attach(yeast)
      triggerobj <- trigger.build(marker = marker, exp = exp,
    					marker.pos = marker.pos, exp.pos = exp.pos)
      crossfile <- trigger.export2cross(triggerobj, plotarg = TRUE, verbose = TRUE, warning = FALSE)
      tt.pval <- trigger.trait(triggerobj, trait  =  "DSE1", cross  =  crossfile)
      causal.reg <- names(which(p.adjust(tt.pval, method = "fdr")<.05))
      detach(yeast)

[Package trigger version 1.28.0 Index]