R: Align Sequences to a Center

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 `sdists`.
`weight` | argument to `sdists`.
`exclude` | arguments to `sdists`.
`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 `x` should be aligned with each other, too.
`to.data.frame` | a logical specifying whether the result should be converted to `data.frame`.

### 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)

[Package cba version 0.2-21 Index]