paraFixSites: The fixation sites with mutation on parallel lineage

In Takkoona/sitePath: Phylogeny-based sequence clustering with site polymorphism

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)

Takkoona/sitePath documentation built on Sept. 28, 2022, 1:24 a.m.