sitesMinEntropy: Fixation sites prediction

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

Fixation sites prediction

Description

After finding the lineagePath of a phylogenetic tree, sitesMinEntropy perform entropy minimization on every site of the sequence to group the tips according to amino acid/nucleotide.

Usage

sitesMinEntropy(x, ...)

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

Arguments

x	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 sitesMinEntropy object.

Examples

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

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