setSiteNumbering {sitePath} | R Documentation

## Set site numbering to the reference sequence

### Description

A reference sequence can be used to define a global site numbering scheme for multiple sequence alignment. The gap in the reference will be skipped so the site ignored in numbering.

### Usage

    ## S3 method for class 'phylo'
    setSiteNumbering(x, reference = NULL, gapChar = "-", ...)

    ## S3 method for class 'lineagePath'
    setSiteNumbering(x, reference = NULL, gapChar = "-", ...)

### Arguments

`x` | The object to set site numbering. It could be a `phylo` object after `addMSA` or a `lineagePath` object. The function for `fixaitonSites` and `multiFixationSites` will be added in later version.
`reference` | Name of reference for site numbering. The name has to be one of the sequences' name. The default uses the intrinsic alignment numbering
`gapChar` | The character to indicate gap. The numbering will skip the gapChar for the reference sequence.
`...` | further arguments passed to or from other methods.

### Value

A `phylo` object with site numbering mapped to reference sequence

### Examples

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

[Package sitePath version 1.2.3 Index]