parallelSites {sitePath} | R Documentation

## Mutation across multiple phylogenetic lineages

### Description

A site may have mutated on parallel lineages. Mutation can occur on the same site across the phylogenetic lineages solved by `lineagePath`. The site will be considered mutated in parallel if the mutation occurs on the non-overlap part of more than two lineages. The amino acid/nucleotide before and after the mutation can be allowed different on different lineages or only the exact same mutations are considered.

### Usage

    parallelSites(x, ...)

    ## S3 method for class 'lineagePath'
    parallelSites(
      x,
      minSNP = NULL,
      mutMode = c("all", "exact", "pre", "post"),
      ...
    )

    ## S3 method for class 'sitesMinEntropy'
    parallelSites(
      x,
      minSNP = NULL,
      mutMode = c("all", "exact", "pre", "post"),
      ...
    )

### Arguments

`x` | A `lineagePath` or a `sitesMinEntropy` object.
`...` | The arguments in `sitesMinEntropy`.
`minSNP` | The minimum number of mutations to be qualified as parallel on at least two lineages. The default is 1.
`mutMode` | The strategy for finding parallel site. The default `all` is to consider any mutation regardless of the amino acid/nucleotide before and after mutation; Or `exact` to force mutation to be the same; Or `pre`/`post` to select the site having amino acid/nucleotide before/after mutation.

### Value

A `parallelSites` object

### Examples

    data(zikv_tree_reduced)
    data(zikv_align_reduced)
    tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
    paths <- lineagePath(tree)
    x <- sitesMinEntropy(paths)
    parallelSites(x)

[Package sitePath version 1.8.4 Index]