allSitesName: Retrieve position of all the sites

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

Retrieve position of all the sites

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 'sitesMinEntropy'
allSitesName(x, ...)

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

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

## S3 method for class 'paraFixSites'
allSitesName(x, type = c("paraFix", "fixation", "parallel"), ...)

Arguments

x	The object containing the sites from analysis
...	Other arguments
type	Return fixation or parallel sites

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)

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