allSitesName: Retrieve position of all the sites

Description Usage Arguments Value Examples

View source: R/allSitesName.R

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

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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

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

wuaipinglab/sitePath documentation built on July 25, 2021, 9:11 p.m.