allSitesName: Retrieve position of all the sites

In sitePath: Detection of site fixation in molecular evolution

Description

The function is a way to get position of the resulting sites from SNPsites, fixationSites and parallelSites. The numbering is consistent with what's being set by setSiteNumbering

Usage

allSitesName(x, ...)

## S3 method for class 'SNPsites'
allSitesName(x, ...)

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

## S3 method for class 'parallelSites'
allSitesName(x, ...)

## S3 method for class 'paraFixSites'
allSitesName(x, ...)

Arguments

x	The object containing the sites from analysis
...	Other arguments

Value

An integer vector for sites position

Examples

data(zikv_tree)
msaPath <- system.file('extdata', 'ZIKV.fasta', package = 'sitePath')
tree <- addMSA(zikv_tree, msaPath = msaPath, msaFormat = 'fasta')
snp <- SNPsites(tree)
allSitesName(snp)

sitePath documentation built on April 17, 2021, 6:05 p.m.