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Thread: New calculator, K7

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    3 members found this post helpful.

    New calculator, K7

    Since no one seems to have posted this yet, Davidski has created a new calculator for determining ANE (Ancestral N Eurasian) admixture. You can download the pertinent files from here http://bga101.blogspot.com/2014/09/e...es-ane-k7.html. To get the admixture proportions, follow the first set of instructions posted by peradam athttp://pastebin.com/VzHw9cuD. Note: you need to change k17.par to Eurogenes_ANE.par in order to get it to work.

    Here are my results:

    8.38% ANE
    1.58% ASE
    33.16% WHG-UHG
    0.31% East_Eurasian
    0.38% West_African
    1.32% East_African
    54.87% ENF

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    Can you help?

    I downloaded the stuff here; http://bga101.blogspot.com/2014/09/e...es-ane-k7.html. I followed all these instructions(http://pastebin.com/VzHw9cuD) and the only part I don't understand is #7-9 where they tell you to write some stuff in an opened R, but I don't know where to write it and exactly what the write(what's in quotes?).

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    Quote Originally Posted by Fire Haired14 View Post
    Can you help?

    I downloaded the stuff here; http://bga101.blogspot.com/2014/09/e...es-ane-k7.html. I followed all these instructions(http://pastebin.com/VzHw9cuD) and the only part I don't understand is #7-9 where they tell you to write some stuff in an opened R, but I don't know where to write it and exactly what the write(what's in quotes?).
    Well you need to download your 23andme raw data and the DIYDodecad and the K17 package via this link: http://pastebin.com/VzHw9cuD
    Then you need to Extract and place the DIYDodecad, K17 & 23andMe files into the same folder. Then Open R and change the directory (File > Change Dir) to the folder where you placed your DIY, K17 & raw data files. Then
    1. Enter this command in R:
    2. source('standardize.r') (with the brackets and everything, from source to the last bracket).
    3. Enter this command but replace X with the name of your raw data file:
    4. standardize('X.txt', company='23andMe')
      1. Enter this command:
      2. system('DIYDodecadWin k17.par') (but change k17.par to Eurogenes_ANE.par in order to get it to work.)


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    Quote Originally Posted by John Doe View Post
    Well you need to download your 23andme raw data and the DIYDodecad and the K17 package via this link: http://pastebin.com/VzHw9cuD
    Then you need to Extract and place the DIYDodecad, K17 & 23andMe files into the same folder. Then Open R and change the directory (File > Change Dir) to the folder where you placed your DIY, K17 & raw data files. Then
    1. Enter this command in R:
    2. source('standardize.r') (with the brackets and everything, from source to the last bracket).
    3. Enter this command but replace X with the name of your raw data file:
    4. standardize('X.txt', company='23andMe')
      1. Enter this command:
      2. system('DIYDodecadWin k17.par') (but change k17.par to Eurogenes_ANE.par in order to get it to work.)

    I have all that stuff downloaded and in the same folder. I opened R, I just don't know how to change the directory, etc. Do they want you to put the address of the file with the downloads, like Libraries>Documents>etc? I tried that and it didn't work. I don't understand where to type the stuff they're telling me to.

    Also, this test is on GEDmatch now but people are already complaining about it;s major differnces with how you did it. Can you get results on GEDmatch and see if there are major differences with the results you have on this thread? I got results on GEDmatch but they seem to have alot of noise.

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    R:
    16.51% ANE
    3.50% ASE
    14.14% WHG-UHG
    5.60% East_Eurasian
    0.51% West_African
    0.64% East_African
    59.09% ENF

    Gedmatch:
    ANE 20.57%
    ASE 5.15%
    WHG-UHG 22.15%
    East_Eurasian 8.42%
    West_African 1.92%
    East_African -
    ENF 41.79%

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    Useless & failed experiment!


    FINAL ADMIXTURE PROPORTIONS:

    ANE - 17.95%
    ASE - 4.54%
    WHG-UHG - 8.00%
    East_Eurasian - 0.00%
    West_African - 0.52%
    East_African - 0.30%
    ENF - 68.69%


    GEDmatch:

    ANE - 21.58%
    ASE - 6.55%

    WHG-UHG - 20.46%
    East_Eurasian - 2.85%
    West_African - 2.13%
    East_African -
    ENF - 46.42%

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    Goga and Icebreaker can one of you guys give me results if I email you 23andme raw data. My uncle's results from GEDmatch seem to be accurate with a little noise. They are very consistent with Eurogenes EEF-WHG-ANE, but it seems that isn't true for most people.

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    Quote Originally Posted by Fire Haired14 View Post
    Goga and Icebreaker can one of you guys give me results if I email you 23andme raw data.
    Sorry, I can't help you because somebody else did the first test for me. But you can ask on this site. I'm sure folks there will help you! http://www.anthrogenica.com/showthre...-Eurogenes-K-6

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    Quote Originally Posted by Goga View Post
    Sorry, I can't help you because somebody else did the first test for me. But you can ask on this site. I'm sure folks there will help you! http://www.anthrogenica.com/showthre...-Eurogenes-K-6
    I was forever banned from that site because of stupid posts, and now the snobbyass moderator will never forgive me and forever hate me and not let me back. Whoever got the results for you can you ask them to do the same for me or give me their email so I can send them raw data?

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    Quote Originally Posted by Fire Haired14 View Post
    I have all that stuff downloaded and in the same folder. I opened R, I just don't know how to change the directory, etc. Do they want you to put the address of the file with the downloads, like Libraries>Documents>etc? I tried that and it didn't work. I don't understand where to type the stuff they're telling me to.

    Also, this test is on GEDmatch now but people are already complaining about it;s major differnces with how you did it. Can you get results on GEDmatch and see if there are major differences with the results you have on this thread? I got results on GEDmatch but they seem to have alot of noise.
    You need to go to the top left and click on file and then click on the change dir, then go to the file you put the raw data and the Dodecad thing in.

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    P.S It's available on Gedmatch now.

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    ANE - 18.78%
    ASE - 3.75%

    WHG-UHG - 41.16%
    East_Eurasian - 3.55%
    West_African - 0.13%
    East_African -
    ENF - 33.02%



    what does this all mean?
    có che un pòpoło no 'l defende pi ła só łéngua el xe prónto par èser s'ciavo

    when a people no longer dares to defend its language it is ripe for slavery.

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    Quote Originally Posted by Fire Haired14 View Post
    I was forever banned from that site because of stupid posts, and now the snobbyass moderator will never forgive me and forever hate me and not let me back. Whoever got the results for you can you ask them to do the same for me or give me their email so I can send them raw data?
    why are you banned, because you are thought to be aggressive when you are direct? ............they mean different things in correspondence

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    Quote Originally Posted by John Doe View Post
    P.S It's available on Gedmatch now.
    so what does mine indicate?

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    Quote Originally Posted by Sile View Post
    why are you banned, because you are thought to be aggressive when you are direct? ............they mean different things in correspondence
    It was for being arrogant and repetitive. I should have been banned in the first place but they should let me back. But whatever it's no big deal.

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    Key to the terms used (from Davidski's blog):
    Ancestral South Eurasian (ASE): this is a really basal cluster that peaks in tribal groups of Southeast Asia. It's probably very similar in some ways to the Ancestral South Indian (ASI) component described by Reich et al. a few years ago.
    Western European/Unknown Hunter-Gatherer (WHG-UHG): this essentially looks like a West Eurasian forager component, and includes the forager-like stuff carried by Neolithic farmers (Oetzi the Iceman has 40% of it).
    Early Neolithic Farmer (ENF): I'd say that this is the component of the earliest Neolithic farmers from the Fertile Crescent.
    The other three components should be easy to work out from their names. They're almost identical to several components with the same or similar names from my other tests.
    Some of you might be wondering why this test doesn't offer an Early European Farmer (EEF) cluster. But the answer to that should be obvious by now. EEF is not a stable ancestral component. It's actually a composite of at least two ancient components, including the so called Basal Eurasian and WHG-UHG. If it really was a genuine ancestral component, like ANE, then I'm pretty sure I'd be able catch it with ADMIXTURE. But I can't.

    My results (via GEDmatch):
    Population
    ANE 10.28%
    ASE 0.79%
    WHG-UHG 46.94%
    East_Eurasian -
    West_African 0.69%
    East_African 0.42%
    ENF 40.87%

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    Quote Originally Posted by Mars View Post
    Key to the terms used (from Davidski's blog):
    Ancestral South Eurasian (ASE): this is a really basal cluster that peaks in tribal groups of Southeast Asia. It's probably very similar in some ways to the Ancestral South Indian (ASI) component described by Reich et al. a few years ago.
    Western European/Unknown Hunter-Gatherer (WHG-UHG): this essentially looks like a West Eurasian forager component, and includes the forager-like stuff carried by Neolithic farmers (Oetzi the Iceman has 40% of it).
    Early Neolithic Farmer (ENF): I'd say that this is the component of the earliest Neolithic farmers from the Fertile Crescent.
    The other three components should be easy to work out from their names. They're almost identical to several components with the same or similar names from my other tests.
    Some of you might be wondering why this test doesn't offer an Early European Farmer (EEF) cluster. But the answer to that should be obvious by now. EEF is not a stable ancestral component. It's actually a composite of at least two ancient components, including the so called Basal Eurasian and WHG-UHG. If it really was a genuine ancestral component, like ANE, then I'm pretty sure I'd be able catch it with ADMIXTURE. But I can't.

    My results (via GEDmatch):
    Population
    ANE 10.28%
    ASE 0.79%
    WHG-UHG 46.94%
    East_Eurasian -
    West_African 0.69%
    East_African 0.42%
    ENF 40.87%
    I get about 30% WHG in this calculator. Ashkenazi Jews don't have WHG outside the EEF, but I suppose if you break the latter you'll get some of that Mesolithic component just like Otzi did.

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    Thanks for the info!

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    ASE 3.08
    WHG-UHG 66.13
    East_Eurasian 1.57
    West_African 0.67
    East_African -
    ENF 12.48

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    Population
    ANE 9.54 Pct
    ASE 1.44 Pct
    WHG-UHG 41.29 Pct
    East_Eurasian 5.57 Pct
    West_African 3.62 Pct
    East_African 13.94 Pct
    ENF 24.60 Pct

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    I think I read somewhere that the whole point of that test is to isolate the ANE and that the rest of the admixture should be ignored.

    Interesting that that my ANE percentage of 13.82% is very close to my Scandinavian 13.8% in a different test on gene plaza. I wonder if the same SNPs were used for both groupings?

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    Attachment 11438 . I don't have much farmer, I guess

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    Lazaridis et al. and Raghavan et al. estimate that the Karitiana Indians (Brazilian Amazon) are at just over 41% ANE.

    Karitiana_HGDP00998
    ANE 41.56%
    ASE 0.41%
    WHG-UHG 0%
    East_Eurasian 58.01%
    West_African 0%
    East_African 0.01%
    ENF 0%

    Lezgin_GSM536850
    ANE 26.74%
    ASE 3.88%
    WHG-UHG 14.65%
    East_Eurasian 0%
    West_African 0.01%
    East_African 0%
    ENF 54.72%

    Bedouin_HGDP00651
    ANE 0%
    ASE 0%
    WHG-UHG 0.05%
    East_Eurasian 1.49%
    West_African 0%
    East_African 8.19%
    ENF 90.27%

    Sardinian_HGDP01067
    ANE 0%
    ASE 0%
    WHG-UHG 49.49%
    East_Eurasian 1.8%
    West_African 0.01%
    East_African 0.01%
    ENF 48.69%

    Source: http://bga101.blogspot.com/2014/09/e...es-ane-k7.html
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