The functions in sitePath usually include the results on
more than one site. The function extractSite can be used to extract
the predicted result on a single site.
extractSite(x, site, ...)
# S3 method for fixationSites
extractSite(x, site, ...)A fixationSites or a parallelSites object. More type
will be supported in the later version.
A site included in the result.
Other arguments
The predicted result of a single site
data(zikv_tree_reduced)
data(zikv_align_reduced)
tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
mutations <- fixationSites(lineagePath(tree))
extractSite(mutations, 139)
#> Site 139 may experience fixation on 1 path(s):
#>
#> S139N (20->72)
#>
#> In the bracket are the number of tips involved before and after the fixation