trigger.export2cross-methods {trigger} | R Documentation |
trigger.export2cross
exports trigger
data from triggerobj
to a cross
format for Trait-Trigger analysis. See trigger.trait
for details.
## S4 method for signature 'trigger' trigger.export2cross(triggerobj, plotarg = TRUE, verbose = TRUE, warning = FALSE)
triggerobj |
An object of class |
plotarg |
Logical. If |
verbose |
Logical. If |
warning |
Logical. If |
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.
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)