trigger-export2cross: Export Trigger data to R/qtl's cross class object

In StoreyLab/trigger-devel: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

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 [e-mail], Dipen P. Sangurdekar [e-mail] and John D. Storey [e-mail]

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)

StoreyLab/trigger-devel documentation built on May 9, 2019, 3:11 p.m.