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 |
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.
1 2 3 4 5 6 7 8 | 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)
|
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