Fixation sites prediction

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.

sitesMinEntropy(x, ...)

# S3 method for 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))
#> This is a 'sitesMinEntropy' object. 
#> 
#> There are 240 sites with enough variation.