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Thread: Mephisto's K15 calculator

  1. #1
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    Mephisto's K15 calculator

    So, this is a calculator I made a while ago from an unsupervised ADMIXTURE run. Some ancestral components which were created seemed absurd to me, but after I created a calculator I saw that the results look pretty good. There were some ancestral components which were basically created by the calculator for few individuals. I used the Behar et al 2010 dataset (I assume they tested very related individuals and thus made a wrong picture of various populations) as well as some individuals from the Human Origins dataset. Most components should be clear expect Med[iterranean]_broad which is found in various populations around the Mediterranean Sea (however not peaking specifically), and ME_broad (Middle East broad) which is an ancestral component peaking in one Jordanian and one Georgian (this was an unsupervised so I did not do this absurdity). Again there is only one Europe component because ADMIXTURE did not see it as relevant to make separated European populations, this time it peaks in East Europeans while Western Europeans should have more of the Mediterranean components. Below are the ADMXITURE graphs:
    f3wwlD9.png
    YftvFqh.png
    I also made a 4admix Oracle file and a nMonte file, however not all samples are named according to their ethnicity, to look those samples up open the samples file and press cntrl + f to search for the samples which popped up in your oracles/or nMonte runs. This are the biggest Oracle and nMonte files ever made.
    Download:
    https://drive.google.com/drive/folde...5V?usp=sharing
    Last edited by mephisto; 04-02-2018 at 03:36 PM.

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  3. #2
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    Can you do mine for me?
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  4. #3
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    It's really annoying when data sets do not separate Romas from Romanians.


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  6. #4
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    Poland
    Cool calc mephisto, my results (>2% in bold):

    0.00% Khomani
    0.00% W_Africa
    1.34% Mozabite
    1.79% Bedouin
    0.00% E_Asia
    0.01% Med_broad
    2.49% Yakut
    7.21% Balochi
    0.54% ME_broad
    7.55% Caucasus
    0.07% Arabian_Pen
    0.00% Papuan
    22.43% Mediterranean
    0.00% E_African
    56.56% Europe
    For K25 and other calculators by me you can send me you raw data to my email: Hidden Content

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  8. #5
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    Quote Originally Posted by Dorkymon View Post
    It's really annoying when data sets do not separate Romas from Romanians.

    Yes, those samples seem to be Romanis. I took the dataset as it was published. I also noticed other strange labelings.
    Last edited by mephisto; 04-02-2018 at 03:59 PM.

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    ----------------------------
    FINAL ADMIXTURE PROPORTIONS:
    ----------------------------

    0.18% Khomani
    0.00% W_Africa
    1.25% Mozabite
    11.05% Bedouin
    0.94% E_Asia
    0.16% Med_broad
    1.78% Yakut
    25.58% Balochi
    1.75% ME_broad
    25.34% Caucasus
    1.04% Arabian_Pen
    0.00% Papuan
    20.57% Mediterranean
    0.30% E_African
    10.07% Europe

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     Lupus82 (04-02-2018),  mephisto (04-02-2018),  michal3141 (04-02-2018)

  12. #7
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    Quote Originally Posted by firemonkey View Post
    Can you do mine for me?
    Code:
      0.00%  Khomani             
      0.00%  W_Africa            
      3.34%  Mozabite            
      1.86%  Bedouin             
      0.32%  E_Asia              
      0.32%  Med_broad           
      1.16%  Yakut               
      7.48%  Balochi             
      0.82%  ME_broad            
      5.31%  Caucasus            
      0.01%  Arabian_Pen         
      0.19%  Papuan              
     24.84%  Mediterranean       
      0.15%  E_African           
     54.19%  Europe
    The nMonte run was weird:
    [1] "distance%=3.0137 / distance=0.030137"

    firemonkey

    hungary3 72.00
    Mordovians1 16.00
    HGDP00525 (French) 7.60
    HGDP00797 (Orcadian) 4.25
    HGDP01078 (Sardinian) 0.15

    To the people wanting to use the files for nMonte: you have to divide your scored value of the various components by 100. As an example: 12,35 (out of the calculator) / 100 = 0,1235, the results is how you should enter the values for the target nMonte file. For admix4 you do not have to do this.
    Last edited by mephisto; 04-02-2018 at 04:21 PM.

  13. #8
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    Quote Originally Posted by mephisto View Post
    Code:
      0.00%  Khomani             
      0.00%  W_Africa            
      3.34%  Mozabite            
      1.86%  Bedouin             
      0.32%  E_Asia              
      0.32%  Med_broad           
      1.16%  Yakut               
      7.48%  Balochi             
      0.82%  ME_broad            
      5.31%  Caucasus            
      0.01%  Arabian_Pen         
      0.19%  Papuan              
     24.84%  Mediterranean       
      0.15%  E_African           
     54.19%  Europe
    The nMonte run was weird:
    [1] "distance%=3.0137 / distance=0.030137"

    firemonkey

    hungary3 72.00
    Mordovians1 16.00
    HGDP00525 (French) 7.60
    HGDP00797 (Orcadian) 4.25
    HGDP01078 (Sardinian) 0.15
    For nMonte I think you should use population averages instead of individual results.
    For K25 and other calculators by me you can send me you raw data to my email: Hidden Content

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    Quote Originally Posted by mephisto View Post
    Code:
      0.00%  Khomani             
      0.00%  W_Africa            
      3.34%  Mozabite            
      1.86%  Bedouin             
      0.32%  E_Asia              
      0.32%  Med_broad           
      1.16%  Yakut               
      7.48%  Balochi             
      0.82%  ME_broad            
      5.31%  Caucasus            
      0.01%  Arabian_Pen         
      0.19%  Papuan              
     24.84%  Mediterranean       
      0.15%  E_African           
     54.19%  Europe
    The nMonte run was weird:
    [1] "distance%=3.0137 / distance=0.030137"

    firemonkey

    hungary3 72.00
    Mordovians1 16.00
    HGDP00525 (French) 7.60
    HGDP00797 (Orcadian) 4.25
    HGDP01078 (Sardinian) 0.15

    To the people wanting to use the files for nMonte: you have to divide your scored value of the various components by 100. As an example: 12,35 (out of the calculator) / 100 = 0,1235, the results is how you should enter the values for the target nMonte file. For admix4 you do not have to do this.

    Does the nMonte suggest a flaw with the calculator?
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  16. #10
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    Tunisia African Union
    Regions of Ancestry
    West Africa - East Africa - North Africa - Levant - Arabia - Southern Europe - South Asia - Oceania - Northern Europe - Asia East

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