fixationSites: 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, fixationSites uses the result to find those sites that show fixation on some, if not all, of the lineages. The number of tips before and after the fixation mutation is expected to be more than minEffectiveSize. Also, the fixation will be skipped if the amino acid/nucleotide is gap or ambiguous character. A lineage has to have at least one fixation mutation to be reported.

Usage

fixationSites(paths, ...)

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

## S3 method for class 'sitesMinEntropy'
fixationSites(paths, ...)

## S3 method for class 'paraFixSites'
fixationSites(paths, ...)

Arguments

paths	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 fixationSites object.

See Also

as.data.frame.fixationSites

Examples

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

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