[R-sig-genetics] extract the sequences of the haplotypes

[Emmanuel Paradis]

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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