distance-methods {haplotypes} | R Documentation |
Calculates absolute pairwise character difference matrix using a Dna
object
Description
Computes and returns an absolute pairwise character difference matrix from DNA sequences.
Usage
## S4 method for signature 'Dna'
distance(x,subset=NULL,indels="sic")
Arguments
x |
an object of class |
subset |
a vector of integers in the range [1,nrow(x)], specifying which sequence(s) are used in the distance calculation. Only distance between selected sequence(s) and the rest of the sequences are calculated. If it is NULL, all comparisons are done. |
indels |
the indel coding method to be used. This must be one of "sic", "5th" or "missing". Any unambiguous substring can be given. See also ‘Details’ |
Details
Available indel coding methods:
sic
:Treating gaps as a missing character and coding them separately following the simple indel coding method.
5th
:Treating gaps as a fifth state character.
missing
:Treating gaps as a missing character.
Value
returns an object of class dist
.
Methods
signature(x = "Dna")
-
Computes and returns an absolute pairwise character difference matrix from
Dna
objects.
Author(s)
Caner Aktas, caktas.aca@gmail.com
References
Giribet, G. and Wheeler, W.C. (1999) On gaps. Molecular Phylogenetics and Evolution 13, 132-143.
Simmons, M., Ochoterena, H. (2000) Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49, 369-381.
See Also
indelcoder
and subs
Examples
data("dna.obj")
x<-dna.obj[4:7,13:22,as.matrix=FALSE]
## Simple indel coding.
distance(x,indels="s")
## Gaps as 5th state characters.
distance(x,indels="5")
## Gaps as missing characters.
distance(x,indels="m")
## Not run:
## Using 'subset'.
x<-dna.obj[4:10,13:22,as.matrix=FALSE]
distance(x, NULL)
distance(x, subset=c(1))
distance(x, subset=c(2,4))
## End(Not run)