extractSite: Extract tips for a single site

In Takkoona/sitePath: Phylogeny-based sequence clustering with site polymorphism

Extract tips for a single site

Description

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.

Usage

extractSite(x, site, ...)

## S3 method for class 'fixationSites'
extractSite(x, site, ...)

Arguments

x	A fixationSites or a parallelSites object. More type will be supported in the later version.
site	A site included in the result.
...	Other arguments

Value

The predicted result of a single site

Examples

data(zikv_tree_reduced)
data(zikv_align_reduced)
tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
mutations <- fixationSites(lineagePath(tree))
extractSite(mutations, 139)

Takkoona/sitePath documentation built on Sept. 28, 2022, 1:24 a.m.