trigger: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1 2	## S4 method for signature 'trigger' trigger.export2cross(triggerobj, plotarg = TRUE, verbose = TRUE, warning = FALSE)

`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.

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.

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

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

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

trigger.trait

  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)