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MSMS error about producing DNA sequence data about locus #206

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QBS024 opened this issue Feb 14, 2020 · 1 comment
Open

MSMS error about producing DNA sequence data about locus #206

QBS024 opened this issue Feb 14, 2020 · 1 comment

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@QBS024
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QBS024 commented Feb 14, 2020

Hello professor,
I am new to your great package. I need use MSMS to generate DNA sequence data.
I write code like this ,

try<-coal_model(10,1,100)+feat_mutation(1.3)+feat_recombination(1.3)+
feat_selection(strength_AA = 8e+3,Ne=4e+5,position=0.5,start=TRUE,time=0.005)+
sumstat_seg_sites()+sumstat_sfs()+sumstat_dna()
But, when I simulate this , simulate(try). I got error like this
" Error in sim_tasks[[i]]$get_arg("trio_dists") :
Argument trio_dists not found"

Could you please give me some idea to fix it? I appreciate your help.
Thanks a lot.

@paulstaab
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You need to use a finite sites mutation model if you want to simulate DNA sequences with sumstat_dna():

  try<-coal_model(10,1,100)+
    feat_mutation(1.3, model = "HKY", tstv_ratio = 2, base_frequencies = c(.25, .25, .25, .25))+
    feat_recombination(1.3)+
    feat_selection(strength_AA = 8e+3,Ne=4e+5,position=0.5,start=TRUE,time=0.005)+
    sumstat_dna()
  simulate(try)

Coala should throw a more helpful error message here.

Also, if you want to calculate ´sumstat_seg_sites()andsumstat_sfs()` with a finite sites mutation model, you need to add an outgroup to your model, please see ´?feat_outgroup()´

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