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 sequence will be skipped for the numbering. Also, the site that is gap or amino acid/nucleotide for too many tips will be ignored but won't affect numbering.

### Usage

    setSiteNumbering(x, reference, gapChar, ...)

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

### Arguments

`x` | The object to set site numbering. It could be a `phyMSAmatched` or a `lineagePath` object.
`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.
`minSkipSize` | The minimum number of tips to have gap or ambiguous amino acid/nucleotide for a site to be ignored in other analysis. This will not affect the numbering. The default is 0.8.

### Value

The input `x` with numbering mapped to `reference`.

### 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 1.8.4 Index]