setSiteNumbering {sitePath} | R Documentation |
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.
## S3 method for class 'phylo' setSiteNumbering(x, reference = NULL, gapChar = "-", ...) ## S3 method for class 'lineagePath' setSiteNumbering(x, reference = NULL, gapChar = "-", ...)
x |
The object to set site numbering. It could be a |
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. |
A phylo
object with site numbering mapped to reference sequence
data(zikv_tree) msaPath <- system.file('extdata', 'ZIKV.fasta', package = 'sitePath') tree <- addMSA(zikv_tree, msaPath = msaPath, msaFormat = 'fasta') setSiteNumbering(tree)