paraFixSites: The fixation sites with mutation on parallel lineage

View source: R/paraFixSites.R

paraFixSitesR 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)

wuaipinglab/sitePath documentation built on June 3, 2022, 5:56 a.m.