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.
fixationSites(paths, ...)
# S3 method for lineagePath
fixationSites(
paths,
minEffectiveSize = NULL,
searchDepth = 1,
method = c("compare", "insert", "delete"),
...
)
# S3 method for sitesMinEntropy
fixationSites(paths, ...)
# S3 method for paraFixSites
fixationSites(paths, ...)A lineagePath object returned from
lineagePath function.
further arguments passed to or from other methods.
The minimum number of tips in a group.
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.
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.
A fixationSites object.
data(zikv_tree_reduced)
data(zikv_align_reduced)
tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
fixationSites(lineagePath(tree))
#> This is a 'fixationSites' object.
#>
#> Result for 3 paths:
#>
#> 784 988 196 139 894 1542 2074 2086 2634 3045
#> No reference sequence specified. Using alignment numbering