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Thread: Differentiation into European components by using admix-n and convex optimization

  1. #1
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    Differentiation into European components by using admix-n and convex optimization

    As a first thing I would like to take the opportunity to present here convex optimization method which I learned from michal3141.
    He made a very useful python script which is beside usual ancestry breakdown capable to make admix-n breakdowns.


    For example, my admix-16 breakdown under all European unscaled individual samples is this:


    ph2ter unscaled admix-16
    -------------- ANCESTRY BREAKDOWN: -------------
    15.450% Ukrainian__Ukrainian13
    12.964% Moldovan__44618757251C01
    11.830% Ukrainian__UKR-1909
    11.746% Russian_Voronez__RussianVoron107
    8.841% Swiss_German__Swiss_German4
    8.070% Polish__Polish17
    5.168% French_Nord__N_18
    4.845% Dutch__Netherlands54
    4.220% Italian_Lombardy__BGD103
    3.204% Romanian__A306
    3.098% Dutch__Netherlands36
    2.921% French_Auvergne__C_13
    2.900% Austrian__Austria14
    2.862% Irish__Irish4
    1.273% Greek_Peloponnese__GreeceNE209
    0.608% Serbian__Serbian_Serbia1
    ------------------------------------------------
    Fit error: 0.0004240142058468694




    I have got an idea to compose from this decomposition the regional European components: Northwestern, Northeastern, Southwestern and Southeastern


    0.0807 Polish__Polish17
    0.11746 Russian_Voronez__RussianVoron107
    0.1183 Ukrainian__UKR-1909
    0.1545 Ukrainian__Ukrainian13
    -------------------
    0.47096 NE-ph2ter


    0.02862 Irish__Irish4
    0.08841 Swiss_German__Swiss_German4
    0.029 Austrian__Austria14
    0.03098 Dutch__Netherlands36
    0.04845 Dutch__Netherlands54
    0.05168 French_Nord__N_18
    -------------------
    0.27714 NW-ph2ter


    0.01273 Greek_Peloponnese__GreeceNE209
    0.12964 Moldovan__44618757251C01
    0.03204 Romanian__A306
    0.00608 Serbian__Serbian_Serbia1
    -------------------
    0.18049 SE-ph2ter


    0.02921 French_Auvergne__C_13
    0.0422 Italian_Lombardy__BGD103
    -------------------
    0.07141 SW-ph2ter


    Then I can from this construct G25 unscaled profiles and make the similarity maps:













    Decomposition and composition can be done in many ways. For example, someone can construct his English, German, Scandinavian or any other component from admix-n runs under the full G25 European spreadsheet.
    Last edited by ph2ter; 11-05-2020 at 08:46 AM.
     
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  3. #2
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    Do you do this for other posters? If, yes, do you require a donation?

    Tx.

    My data:
     

    Code:
    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC12,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC22,PC23,PC24,PC25
    dosas_scaled,0.106994,0.139128,-0.017348,-0.031008,0.003077,-0.015618,0.004935,0.002308,-0.022907,0.005103,0.003085,0.002698,-0.011447,0.011973,-0.015472,-0.005701,0.007041,0.00114,0.002514,-0.005002,-0.003369,0.002473,-0.002218,0.003735,-0.003712
    
    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC12,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC22,PC23,PC24,PC25
    dosas,0.0094,0.0137,-0.0046,-0.0096,0.001,-0.0056,0.0021,0.001,-0.0112,0.0028,0.0019,0.0018,-0.0077,0.0087,-0.0114,-0.0043,0.0054,0.0009,0.002,-0.004,-0.0027,0.002,-0.0018,0.0031,-0.0031

  4. #3
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    Quote Originally Posted by dosas View Post
    Do you do this for other posters? If, yes, do you require a donation?

    Tx.

    My data:
     

    Code:
    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC12,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC22,PC23,PC24,PC25
    dosas_scaled,0.106994,0.139128,-0.017348,-0.031008,0.003077,-0.015618,0.004935,0.002308,-0.022907,0.005103,0.003085,0.002698,-0.011447,0.011973,-0.015472,-0.005701,0.007041,0.00114,0.002514,-0.005002,-0.003369,0.002473,-0.002218,0.003735,-0.003712
    
    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC12,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC22,PC23,PC24,PC25
    dosas,0.0094,0.0137,-0.0046,-0.0096,0.001,-0.0056,0.0021,0.001,-0.0112,0.0028,0.0019,0.0018,-0.0077,0.0087,-0.0114,-0.0043,0.0054,0.0009,0.002,-0.004,-0.0027,0.002,-0.0018,0.0031,-0.0031
    Yes and yes

    I can make only a breakdown for free.



    dosas unscaled admix-16
    -------------- ANCESTRY BREAKDOWN: -------------
    24.080% Greek_Trabzon__G25003
    14.716% Greek_Izmir__GreeceSmyrna9
    8.091% Albanian__ALB220
    7.174% Greek_Trabzon__G25001
    6.939% Greek_Trabzon__G25005
    6.814% Albanian__ALB212
    6.095% Albanian__ALB191
    5.321% Albanian__AL12
    5.164% Roma_Bilbao__Alg12
    4.997% Turkish_Kayseri__Kayseri23271
    4.419% Polish__Polish9
    2.221% Albanian__AL98
    1.212% Mordovian__MOE-445
    1.103% Lithuanian_PA__LTG-788
    0.972% Moldovan__44618758491C02
    0.682% Greek_Trabzon__G25002
    ------------------------------------------------
    Fit error: 0.004490800729930287
    Last edited by ph2ter; 11-05-2020 at 09:01 AM.
     
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  6. #4
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    Michal breakdowns with admix-16

    -------------- ANCESTRY BREAKDOWN: -------------
    18.712% Russian_Kostroma__RUS_Kostr138
    17.749% Latvian__latvian54A2
    15.856% Moldovan_o__Moldovan_V13693
    13.499% Ukrainian__UKR-1283
    10.514% German__German71
    6.881% Lithuanian_RA__LTG-26
    5.514% Polish__Polish23
    2.533% Moldovan_o__Moldovan_V46055
    2.284% Spanish_Galicia__GAL26
    2.223% Sardinian__HGDP01066
    2.145% Ashkenazi_Lithuania__Ashk_LT_LT_5
    0.784% Macedonian__Macedonian2
    0.764% Italian_Aosta_Valley__Aosta17
    0.358% Lithuanian_RA__LTG-64
    0.183% Greek_Central_Macedonia__GreeceNE34
    ------------------------------------------------
    Fit error: 0.004454161033559039


    0.18712 Russian_Kostroma__RUS_Kostr138
    0.17749 Latvian__latvian54A2
    0.06881 Lithuanian_RA__LTG-26
    0.00358 Lithuanian_RA__LTG-64
    ------
    0.437 michal_Baltic


    0.05514 Polish__Polish23
    0.13499 Ukrainian__UKR-1283
    0.15856 Moldovan_o__Moldovan_V13693
    0.02533 Moldovan_o__Moldovan_V46055
    -----
    0.37402 michal_Polish-Ukrainian


    0.10514 German__German71
    ------
    0.10514 michal_NW


    0.00183 Greek_Central_Macedonia__GreeceNE34
    0.00784 Macedonian__Macedonian2
    0.02223 Sardinian__HGDP01066
    0.02284 Spanish_Galicia__GAL26
    0.02145 Ashkenazi_Lithuania__Ashk_LT_LT_5
    0.00764 Italian_Aosta_Valley__Aosta17
    ------
    0.08383 michal_Southern

    The maps:



     
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    Could you do breakdown for me please? Thanks in advance

    Cyryl_scaled,0.134311,0.127957,0.053174,0.047158,0 .033852,0.014781,0.006345,0.005077,-0.004295,-0.015308,0.005846,-0.010641,0.014569,0.01156,-0.015472,0.000398,0.001825,-0.000633,-0.000754,0.001126,-0.006613,-0.007543,0.003328,-0.001084,0.005748

    Cyryl,0.0118,0.0126,0.0141,0.0146,0.011,0.0053,0.0 027,0.0022,-0.0021,-0.0084,0.0036,-0.0071,0.0098,0.0084,-0.0114,0.0003,0.0014,-0.0005,-0.0006,0.0009,-0.0053,-0.0061,0.0027,-0.0009,0.0048

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    Tim_scaled,0.129758,0.129988,0.064865,0.047481,0.0 437,0.02008,0.002115,0.003231,0.007158,-0.000547,-0.002598,0.004496,-0.010555,-0.01101,0.028366,0.006364,-0.021513,0.005701,0.001508,0.001501,0.004742,0.001 731,-0.002465,0.008796,-0.003473

    Tim,0.0114,0.0128,0.0172,0.0147,0.0142,0.0072,0.00 09,0.0014,0.0035,-0.0003,-0.0016,0.003,-0.0071,-0.008,0.0209,0.0048,-0.0165,0.0045,0.0012,0.0012,0.0038,0.0014,-0.002,0.0073,-0.0029

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  14. #8
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    Quote Originally Posted by RVBLAKE View Post
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    Thanky ou very much!

    Here are your results:

    RVBLAKE unscaled convex optimization method admix-16


    -------------- ANCESTRY BREAKDOWN: -------------
    25.778% German__German14
    14.783% English__HG02215
    11.091% English__English1
    10.594% German__German35
    8.614% Dutch__Netherlands54
    8.428% Spanish_Peri-Barcelona__CAL053
    4.349% English__England13
    4.116% German__German11
    3.657% English_Cornwall__HG00253
    3.360% Finnish_East__HG00323
    1.553% English__English3
    1.309% Spanish_Aragon__HG01678
    1.040% Sardinian__HGDP00674
    0.574% Italian_Lombardy__BGD103
    0.439% Polish__Polish17
    0.315% Finnish__HG00277
    ------------------------------------------------
    Fit error: 0.0037918324994111042


    0.03657 English_Cornwall__HG00253
    0.04349 English__England13
    0.11091 English__English1
    0.01553 English__English3
    0.14783 English__HG02215
    0.35433 RVBLAKE-English_35.433

    0.0336 Finnish_East__HG00323
    0.00315 Finnish__HG00277
    0.00439 Polish__Polish17
    0.04114 RVBLAKE-NE_4.114

    0.08614 Dutch__Netherlands54
    0.04116 German__German11
    0.25778 German__German14
    0.10594 German__German35
    0.49102 RVBLAKE-German_49.102

    0.00574 Italian_Lombardy__BGD103
    0.0104 Sardinian__HGDP00674
    0.01309 Spanish_Aragon__HG01678
    0.08428 Spanish_Peri-Barcelona__CAL053
    0.11351 RVBLAKE-SW_11.351










    Code:
    RVBLAKE-English_35.433,0.011373045,0.014020116,0.018393168,0.01354705,0.01479405,0.005858588,0.002890582,0.001262582,0.004199674,0.003132338,-0.001242469,0.005919478,-0.007141416,-0.002435007,0.016878322,-0.006351988,-0.018931991,0.004040339,0.004143407,0.00168358,0.005039299,0.005611721,-0.001831825,0.010147508,0.002617627
    RVBLAKE-NE_4.114,0.011210019,0.009027842,0.025321864,0.023573099,0.012077639,0.009908903,0.006966889,0.005249576,0.003038339,-0.013415737,0.003190478,-0.003293316,0.013052001,0.012078103,0.004872684,-0.00963977,-0.014854598,0.002073597,0.002395971,0.00122291,0.003861466,0.00181244,0.001153435,0.00940168,0.000126693
    RVBLAKE-German_49.102,0.01114794,0.013725604,0.014424031,0.009716971,0.013893873,0.007318423,0.001979252,0.001063894,0.002764613,0.003581891,-0.005465526,0.003895888,-0.002429975,0.003044833,0.009852826,-0.01163775,-0.017896615,0.005341592,0.004455363,0.002621784,-0.001732176,-0.001384906,0.006582703,0.006819144,-0.000176889
    RVBLAKE-SW_11.351,0.010863773,0.016054101,0.011096113,-0.002115677,0.017090835,-0.000669703,0.001024669,-0.001645066,0.011703393,0.022740393,-0.00268989,0.008176192,-0.015966657,-0.00378091,0.005982797,-0.00914767,-0.014915989,0.004072331,0.006568797,-0.00206327,0.001798057,0.00368295,-0.006436618,-0.002041123,-0.002165976
    vahaduo check:
    Target: RVBLAKE
    Distance: 0.0025% / 0.00002519
    49.0 RVBLAKE-German_49.102
    35.4 RVBLAKE-English_35.433
    11.4 RVBLAKE-SW_11.351
    4.2 RVBLAKE-NE_4.114
    Last edited by ph2ter; 11-05-2020 at 12:41 PM.
     
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  16. #9
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    Thanks ph2ter!
    Very nice maps. I wonder if you could also do similar breakdown with scaled coordinates and some penalty like pen=0.001

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  18. #10
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    Quote Originally Posted by michal3141 View Post
    Thanks ph2ter!
    Very nice maps. I wonder if you could also do similar breakdown with scaled coordinates and some penalty like pen=0.001
    I will do that later especially for you. Why penalty?
     
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