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

Susana susana.campino at lshtm.ac.uk
Wed Apr 27 02:32:05 CEST 2016


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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