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 1.4.2 Index]