haplotype {pegas} | R Documentation |
haplotype
extracts the haplotypes from a set of DNA
sequences. The result can be plotted with the appropriate function.
haplotype(x, labels = NULL) ## S3 method for class 'haplotype': plot(x, ...) ## S3 method for class 'haplotype': print(x, ...)
x |
a set of DNA sequences (as an object of class
"DNAbin" , or an object of class "haplotype" . |
labels |
a vector of character strings used as names for the rows of the returned object. By default, Roman numerals are given. |
... |
further arguments passed to
barplot (unused in print ). |
haplotype
returns an object of class c("haplotype",
"DNAbin")
which is an object of class "DNAbin"
with two
additional attributes: "index"
identifying the index of each
observation that share the same haplotype, and "from"
giving
the name of the original data.
Emmanuel Paradis
haploNet
, DNAbin
for manipulation of
DNA sequences in R.
## generate some artificial data from 'woodmouse': data(woodmouse) x <- woodmouse[sample(15, size = 110, replace = TRUE), ] (h <- haplotype(x)) ## the indices of the individuals belonging to the 1st haplotype: attr(h, "index")[[1]]