R: Prepare data for sitePath analysis

addMSA {sitePath}

R Documentation

Prepare data for sitePath analysis

Description

sitePath requires both tree and sequence alignment to do the analysis. addMSA wraps read.alignment function in seqinr package and helps match names in tree and sequence alignment. Either provide the file path to an alignment file and its format or an alignment object from the return of read.alignment function. If both the file path and alignment object are given, the function will use the sequence in the alignment file.

Usage

addMSA(tree, msaPath = "", msaFormat = "", alignment = NULL)

Arguments

`tree`	a `phylo` object. This commonly can be from tree parsing function in `ape` or `ggtree`. All the `tip.label` should be found in the sequence alignment.
`msaPath`	The file path to the multiple sequence alignment file
`msaFormat`	The format of the multiple sequence alignment file
`alignment`	an `alignment` object. This commonly can be from sequence parsing function in the `seqinr` package. Sequence names in the alignment should include all `tip.label` in the tree

Value

addMSA returns a phylo object with matched multiple sequence alignment

Examples

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

[Package sitePath version 1.4.2 Index]