paraFixSites {sitePath} | R Documentation |
The operation between the results of fixationSites
and parallelSites
.
paraFixSites(x, ...) ## S3 method for class 'lineagePath' paraFixSites( x, category = c("intersect", "union", "parallelOnly", "fixationOnly"), minEffectiveSize = NULL, searchDepth = 1, method = c("compare", "insert", "delete"), minSNP = NULL, mutMode = c("all", "exact", "pre", "post"), ... ) ## S3 method for class 'sitesMinEntropy' paraFixSites( x, category = c("intersect", "union", "parallelOnly", "fixationOnly"), minSNP = NULL, mutMode = c("all", "exact", "pre", "post"), ... )
x |
A |
... |
further arguments passed to or from other methods. |
category |
Could be |
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. |
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. |
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 |
A paraFixSites
object.
data(zikv_tree_reduced) data(zikv_align_reduced) tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced) paraFixSites(lineagePath(tree))