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 'phylo'
    paraFixSites(
      x,
      alignment = NULL,
      seqType = c("AA", "DNA", "RNA"),
      Nmin = NULL,
      reference = NULL,
      gapChar = "-",
      minSkipSize = NULL,
      ...
    )

    ## S3 method for class 'treedata'
    paraFixSites(x, ...)

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

    ## 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.
`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
`seqType` | The type of the sequence in the alignment file. The default is "AA" for amino acid. The other options are "DNA" and "RNA".
`Nmin` | The parameter for identifying phylogenetic pathway using SNP. If provided as fraction between 0 and 1, then the minimum number of SNP will be total tips times `Nmin`. If provided as integer greater than 1, the minimum number will be `Nmin`.
`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.
`minSkipSize` | The minimum number of tips to have gap or ambiguous amino acid/nucleotide for a site to be ignored in other analysis. This will not affect the numbering. The default is 0.8.
`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.
`category` | Could be `parallelOnly`, `fixationOnly`, `intersect` or `union`.
`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)
    paraFixSites(zikv_tree_reduced, alignment = zikv_align_reduced)

[Package sitePath version 1.10.2 Index]