fixationSites {sitePath} | R Documentation

## Fixation sites prediction

### Description

After finding the `lineagePath` of a phylogenetic tree, `fixationSites` uses the result to find those sites that show fixation on some, if not all, of the lineages. The number of tips before and after the fixation mutation is expected to be more than `minEffectiveSize`. Also, the fixation will be skipped if the amino acid/nucleotide is gap or ambiguous character. A lineage has to have at least one fixation mutation to be reported.

### Usage

    fixationSites(paths, ...)

    ## S3 method for class 'lineagePath'
    fixationSites(
      paths,
      minEffectiveSize = NULL,
      searchDepth = 1,
      method = c("compare", "insert", "delete"),
      ...
    )

    ## S3 method for class 'sitesMinEntropy'
    fixationSites(paths, ...)

    ## S3 method for class 'paraFixSites'
    fixationSites(paths, ...)

### Arguments

`paths` | A `lineagePath` object returned from `lineagePath` function.
`...` | further arguments passed to or from other methods.
`minEffectiveSize` | The minimum number of tips in a group.
`searchDepth` | The function uses heuristic search but the termination of the search cannot be intrinsically decided. `searchDepth` is needed to tell the search when to stop.
`method` | The strategy for predicting the fixation. The basic approach is entropy minimization and can be achieved by adding or removing fixation point, or by comparing the two.

### Value

A `fixationSites` object.

### See Also

`as.data.frame.fixationSites`

### Examples

    data(zikv_tree_reduced)
    data(zikv_align_reduced)
    tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
    fixationSites(lineagePath(tree))

[Package sitePath version 1.10.2 Index]