unique-methods {haplotypes} | R Documentation |
Extract Unique Sequences
Description
unique
returns a list with duplicate sequences removed.
Usage
## S4 method for signature 'Dna'
unique(x,gaps=FALSE)
Arguments
x |
an object of class |
gaps |
boolean; gaps are removed if this is FALSE. |
Details
This function behaves somehow similar to haplotype
, however indels and missing characters are not taken into account.
Methods
signature(x = "Dna")
Examples
data("dna.obj")
x<-dna.obj[1:6,,as.matrix=FALSE]
##gaps removed.
unique(x)
##gaps not removed.
unique(x,gaps=TRUE)
##unique vs. haplotype
#unique returns 5 unique sequences.
unique(x)
length(unique(x))
#haplotype returns 4 unique haplotypes with simple indel coding.
h<-haplotype(x)
as.list(as.dna(h))
length(h)
#haplotype returns 3 unique haplotypes with gaps as missing.
h<-haplotype(x, indels="m")
as.list(as.dna(h))
length(h)
[Package haplotypes version 1.1.3.1 Index]