sdists.center.align {cba} | R Documentation |
Align Sequences to a Center
Description
Find a global alignment of a collection of sequences using the center-star-tree heuristic.
Usage
sdists.center.align(x, center, method = "ow", weight = c(1, 1, 0, 2),
exclude = c(NA, NaN, Inf, -Inf),
break.ties = TRUE, transitive = FALSE,
to.data.frame = FALSE)
Arguments
x |
a list (of vectors) or a vector of character. |
center |
a vector |
method |
argument to |
weight |
argument to |
exclude |
arguments to |
break.ties |
a logical specifying whether random tie-breaking should be performed. Otherwise the first alignment is used. |
transitive |
a logical specifying whether the sequences in
|
to.data.frame |
a logical specifying whether the result should
be converted to |
Details
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.
Value
Either a list of sequences with attributes center
and
ties
, or a data.frame
with the sequences in
the columns.
Note
The global alignment may depend on the order of x
.
Author(s)
Christian Buchta
References
D. Gusfield (1997). Algorithms on Strings, Trees, and Sequences. Cambridge University Press, Chapter XX.
See Also
sdists
for computation of distances,
sdists.center
for computation of centroids.
Examples
## continue example
x <- c("ABCD", "AD", "BCD", "ACF", "CDF", "BC")
sdists.center.align(x)
sdists.center.align(x, transitive = TRUE, to.data.frame = TRUE)