extractTips {sitePath} | R Documentation |
The result of fixationSites
contains all the possible sites
with fixation mutation. The function extractTips
retrieves
the name of the tips involved in the fixation.
The function extractSite
can be used to extract the fixation info
of a single site.
## S3 method for class 'fixationSites' extractTips(x, site, select = 1, ...) ## S3 method for class 'multiFixationSites' extractTips(x, site, select = 1, ...) ## S3 method for class 'sitePath' extractTips(x, select = 1, ...) ## S3 method for class 'fixationSites' extractSite(x, site, ...) ## S3 method for class 'multiFixationSites' extractSite(x, site, ...)
x |
A |
site |
A site predicted to experience fixation. |
select |
For a site, there theoretically might be more than one fixation on different lineages. You may use this argument to extract for a specific fixation of a site. The default is the first fixation of the site. |
... |
Other arguments |
The function extractTips
returns the name of the
tips involved in the fixation.
The function extractSite
returns a sitePath
object
data(zikv_tree_reduced) data(zikv_align_reduced) tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced) mutations <- fixationSites(lineagePath(tree)) extractTips(mutations, 139) extractSite(mutations, 139)