allSitesName {sitePath} | R Documentation

## 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)

[Package sitePath version 1.10.2 Index]