| sdists.center.align {cba} | R Documentation |
Find a global alignment of a collection of sequences using the center-star-tree heuristic.
sdists.center.align(x, center, method = "ow", weight = c(1, 0, 2),
exclude = c(NA, NaN, Inf, -Inf), break.ties = TRUE,
transitive = FALSE, to.data.frame = FALSE)
x |
a list (of vectors) or a vector of character. |
center |
a vector |
method |
argument to sdists. |
weight |
argument to sdists. |
exclude |
arguments to sdists. |
break.ties |
a logical specifying whether random tie-breaking should be perforemd. Otherwise the first alignment is used. |
transitive |
a logical specifiying whether the sequences in
x should be aligned with each other, too. |
to.data.frame |
a logical specifying whether the result should
be converted to data.frame. |
Each component of x is aligned with center in turn
such that the latter is aligned with all sequences processed so
far.
If center is missing isdists.center is used
to compute an initial center.
Either a list of sequences with attributes center and
ties, or a data.frame with the sequences in
the columns.
The global alignment may depend on the order of x.
Christian Buchta
D. Gusfield (1997). Algorithms on Strings, Trees, and Sequences. Cambridge University Press, Chapter XX.
sdists for computation of distances,
sdists.center for computation of centroids.
## continue example
x <- c("ABCD", "AD", "BCD", "ACF", "CDF", "BC")
sdists.center.align(x)
sdists.center.align(x, transitive = TRUE, to.data.frame = TRUE)