trigger.link-methods {trigger} | R Documentation |
A method of class trigger
for genomewide Expression-trait QTL analysis. This function estimates the linkage statistic and parametric p-value for each gene expression to every locus in the genome.
## S4 method for signature 'trigger' trigger.link(triggerobj, gender = NULL, norm = TRUE)
triggerobj |
An object of class |
gender |
Optional. When computing linkage statistics involving markers on sex chromosome, |
norm |
Logical. If |
An updated object of class trigger
containing slots:
stat |
A matrix of pair-wise likelihood ratio statistics for linkage analysis, with genes in rows and markers in columns. |
pvalue |
A matrix of parametric pvalues corresponding to statistics in the |
Use slot(triggerobj, "stat")
and slot(triggerobj, "pvalue")
to retrieve the values.
Lin S. Chen lschen.stat@gmail.com, Dipen P. Sangurdekar dps@genomics.princeton.edu and John D. Storey jstorey@princeton.edu
plot and trigger.mlink
## Not run: data(yeast) attach(yeast) triggerobj <- trigger.build(marker = marker, exp = exp, marker.pos = marker.pos, exp.pos = exp.pos) triggerobj <- trigger.link(triggerobj, gender = NULL, norm = TRUE) plot(triggerobj,type = "link", cutoff = 1e-5) stat = slot(triggerobj, "stat"); pvalue = slot(triggerobj, "pvalue") detach(yeast) ## End(Not run)