paraFixSites {sitePath} | R Documentation

## The fixation sites with mutation on parallel lineage

### Description

The operation between the results of `fixationSites` and `parallelSites`.

### Usage

    paraFixSites(x, ...)

    ## S3 method for class 'lineagePath'
    paraFixSites(
      x,
      category = c("intersect", "union", "parallelOnly", "fixationOnly"),
      minEffectiveSize = NULL,
      searchDepth = 1,
      method = c("compare", "insert", "delete"),
      minSNP = NULL,
      mutMode = c("all", "exact", "pre", "post"),
      ...
    )

    ## S3 method for class 'sitesMinEntropy'
    paraFixSites(
      x,
      category = c("intersect", "union", "parallelOnly", "fixationOnly"),
      minSNP = NULL,
      mutMode = c("all", "exact", "pre", "post"),
      ...
    )

### Arguments

`x` | A `lineagePath` object returned from `lineagePath` function.
`...` | further arguments passed to or from other methods.
`category` | Could be `parallelOnly`, `fixationOnly`, `intersect` or `union`.
`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.
`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 `paraFixSites` object.

### Examples

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

[Package sitePath version 1.8.4 Index]