Hi Susana,
In fact, the output of haplotype() _are_ the sequences of the haplotypes
(= the unique sequences from your "finaldna" object). It has an
additional attribute which is a list named "index" giving the indices of
individuals belonging to each haplotype (so in your case a list with 27
vectors). So you can, for instance, write these sequences in a file:
h <- haplotype(finaldna)
write.dna(h, "h.txt")
Best,
Emmanuel
Le 27/04/2016 02:32, Susana a écrit :
Hi,
I have a vector with DNA sequences and I created the haplotypes using the
haplotype function in Pegas.
I would like to extract the sequences of the haplotypes, but I can to it. the
object it creates says:
Haplotypes extracted from: finaldna
Number of haplotypes: 27
Sequence length: 20
Haplotype labels and frequencies:
I II III IV V VI VII VIII IX X XI
9 33 329 219 105 1000 1159 14 3 5 24
XII XIII XIV XV XVI XVII XVIII XIX XX XXI XXII
60 10 1 30 1 7 11 2 3 8 4
XXIII XXIV XXV XXVI XXVII
1 1 25 9 9
So, how can I get the sequences from these 27 haplotypes?
Already tried data.frame but it does not work:"cannot coerce class "c("haplotype",
"DNAbin")" to a data.frame"
Any help will be appreciated!
Thanks!
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