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Thread: Post your Eurogenes K13 Admixture Proportions by Chromosome

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    Default Post your Eurogenes K13 Admixture Proportions by Chromosome

    Post your Eurogenes K13 Admixture Proportions by Chromosome from GEDmatch


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    qpAdm: Bulgarian_1.DG= 77 - Kimak.SG= 23, p= 0.36, se= 0.31.
    Y: Q-L330 > Q-YP771 > Q-BZ180 > Q-F16045* (F15008*) --> Baikal N, Altai MLBA, Aldy-Bel, Pazyryk, Hun.
    MT: K1a --> Iron Gates, Starcevo, Bulgaria N, Bulgaria CA, Bulgaria BA.

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    I did nMonte3 analysis to myself by using the default unmodified spreadsheet from GEDmatch.
    csv files (Eurogenes K13) for the R tool can be downloaded here: https://ufile.io/ep9m7

    Spoiler!

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    Quote Originally Posted by Lemgrant View Post
    I did nMonte3 analysis to myself by using the default unmodified spreadsheet from GEDmatch.
    csv files (Eurogenes K13) for the R tool can be downloaded here: https://ufile.io/ep9m7

    Spoiler!
    I did it with MDLPK23b, try to make a PCA to this nMonte. It would be much more interesting.
    qpAdm: Bulgarian_1.DG= 77 - Kimak.SG= 23, p= 0.36, se= 0.31.
    Y: Q-L330 > Q-YP771 > Q-BZ180 > Q-F16045* (F15008*) --> Baikal N, Altai MLBA, Aldy-Bel, Pazyryk, Hun.
    MT: K1a --> Iron Gates, Starcevo, Bulgaria N, Bulgaria CA, Bulgaria BA.

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    Quote Originally Posted by Lemgrant View Post
    I did nMonte3 analysis to myself by using the default unmodified spreadsheet from GEDmatch.
    csv files (Eurogenes K13) for the R tool can be downloaded here: https://ufile.io/ep9m7

    Spoiler!
    Any guides on how to do this? I could never get the PC clients running and this sounds cool af.

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    Quote Originally Posted by Ayetooey View Post
    Any guides on how to do this? I could never get the PC clients running and this sounds cool af.
    Download R software https://cran.r-project.org/bin/windows/base/

    Download csv files for K13: https://ufile.io/ep9m7
    Download csv and nMonte3 files for puntDNAL_K15 and MDLP_k23b https://uploadfiles.io/nzbh7

    Extract the eurogenes_k13.zip and nMonte3.zip

    Copy/paste the nMonte3.R file in the eurogenes_k13 folder

    Launch the R program
    Select File > Change dir... > Browse for eurogenes_k13 folder

    In R console type: source('nMonte3.R')

    Open the testk13.csv with Microsoft Excel or Notepad and change the values according to your values for some specific Chromosome and save the file.

    In R console type: getMonte('eurok13.csv', 'testk13.csv')

    You will get results with default penalty=0.001

    If you want to see results with pen=0, then type getMonte('eurok13.csv', 'testk13.csv', pen=0)


    To see your Eurogenes K13 Admixture Proportions by Chromosome > login to GEDmatch > select Admixture (heritage) > select Admixture Proportions by Chromosome > Eurogenes > K13

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    Quote Originally Posted by Ayetooey View Post
    Any guides on how to do this? I could never get the PC clients running and this sounds cool af.
    So, did you do it or not yet?

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    Quote Originally Posted by Lemgrant View Post
    So, did you do it or not yet?
    No not yet I'm bit busy tonight with a deadline, gonna try it out tomorrow.

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    Quote Originally Posted by Lemgrant View Post
    So, did you do it or not yet?
    I filled out the whole thing line by line and it just gave my my overall k13 average, didn't split it up into seperate chomosome. I deleted it all and did one chromosome separately, still looks wrongish.

    [1] "1. CLOSEST SINGLE ITEM DISTANCE%"
    Romanian Serbian Bulgarian Moldavian Hungarian
    8.700386 9.047030 11.133980 14.247373 14.502830
    Austrian Croatian Greek_Thessaly
    16.074058 16.980453 18.695314

    [1] "2. FULL TABLE nMONTE"
    Error in if (eval2 <= eval1) { : missing value where TRUE/FALSE needed
    In addition: Warning message:
    In sweep(mySel, 2, myTg, "-") :
    STATS is longer than the extent of 'dim(x)[MARGIN]'

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    Quote Originally Posted by Ayetooey View Post
    I filled out the whole thing line by line and it just gave my my overall k13 average, didn't split it up into seperate chomosome. I deleted it all and did one chromosome separately, still looks wrongish.

    [1] "1. CLOSEST SINGLE ITEM DISTANCE%"
    Romanian Serbian Bulgarian Moldavian Hungarian
    8.700386 9.047030 11.133980 14.247373 14.502830
    Austrian Croatian Greek_Thessaly
    16.074058 16.980453 18.695314

    [1] "2. FULL TABLE nMONTE"
    Error in if (eval2 <= eval1) { : missing value where TRUE/FALSE needed
    In addition: Warning message:
    In sweep(mySel, 2, myTg, "-") :
    STATS is longer than the extent of 'dim(x)[MARGIN]'
    What do mean line by line? It is by column.
    You need to edit only those values

    With what program you opened the csv file?

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