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Thread: Eurogenes Project thread.

  1. 05-17-2015, 01:38 AM #531
    surbakhunWeesste
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    Quote Originally Posted by ZephyrousMandaru View Post

    "Error in read.table(file = file, header = header, sep = sep, quote = quote, :
    duplicate 'row.names' are not allowed"
    Code:
    tVec <- read.table(file = target, head = TRUE, sep = "\t", row.names = 1)
    in R file is reading your target.txt file. Its sensitive to whitespace as well. You need to space each entry with a tab.
    The error is perhaps because of multiple header(ANE/WHG....) entries.

    Code:
    	Oceanian_purple	Central_Asian_teal	European_blue	Amerindian_pink	South_Asian_light_green	EEF_orange	East_Asian_yellow	Siberian_crimson	Sub.Saharan_light_blue
Polish	0.005857 	0.43027  	0.012981 	0.020237 	0.143712	 0.328508	1E-005 	1E-005	0.058415
    I created my own target.txt file and even followed the 'syntax' but had trouble as well. I just copy pasted each population to the provided sample target.txt file.

    Unless your issue is with .csv file.
    Last edited by surbakhunWeesste; 05-17-2015 at 01:50 AM.
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  3. 05-17-2015, 02:21 AM #532
    Kurd
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    Quote Originally Posted by zahra View Post
    [CODE]tVec <- read.table(file = target, head = TRUE, sep = "\t", row.names = 1).
    I was curious, did you have to add the above command to run your file. The reason being is that in R that command is an instruction to create a file called tVec from your results file (target) which appears to be not comma separated (likely tab)

    Zephs problem is probably with his Eurogenes spreadsheet having duplicate pop labels
    Last edited by Kurd; 05-17-2015 at 02:30 AM.
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  4. 05-17-2015, 02:38 AM #533
    jesus
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    K8 results:

    Code:
    [1] Target 	 88% Iranian + 5% Maasai + 2% Pathan + 4.99999999999999% South_Indian @ D 	0.0111
[1] Target 	 0% Kurdish + 89% Iranian + 5% Maasai + 5.99999999999999% South_Indian @ D 	0.0113
[1] Target 	 0% Azeri + 89% Iranian + 5% Maasai + 5.99999999999999% South_Indian @ D 	0.0113
[1] Target 	 89% Iranian + 0% Afghan_Pashtun + 5% Maasai + 5.99999999999999% South_Indian @ D 	0.0113
[1] Target 	 89% Iranian + 5% Maasai + 0% Tadjik_Ishkashim + 5.99999999999999% South_Indian @ D 	0.0113
[1] Target 	 89% Iranian + 5% Maasai + 0% Druze + 5.99999999999999% South_Indian @ D 	0.0113
[1] Target 	 89% Iranian + 5% Maasai + 0% Lebanese_Muslim + 5.99999999999999% South_Indian @ D 	0.0113
[1] Target 	 89% Iranian + 5% Maasai + 0% Yamnaya + 5.99999999999999% South_Indian @ D 	0.0113
[1] Target 	 89% Iranian + 5% Maasai + 0% Lezgin + 5.99999999999999% South_Indian @ D 	0.0113
[1] Target 	 89% Iranian + 5% Maasai + 0% South_Italian + 5.99999999999999% South_Indian @ D 	0.0113
[1] Target 	 89% Iranian + 5% Maasai + 5.99999999999999% South_Indian + 0% Georgian_Laz @ D 	0.0113
[1] Target 	 72% Iranian + 5% Maasai + 14% Pathan + 9% Druze @ D 	0.013
[1] Target 	 77% Iranian + 5% Maasai + 12% Pathan + 5.99999999999999% Lebanese_Muslim @ D 	0.0134
[1] Target 	 0% Kurdish + 86% Iranian + 5% Maasai + 9% Pathan @ D 	0.0139
[1] Target 	 0% Azeri + 86% Iranian + 5% Maasai + 9% Pathan @ D 	0.0139
[1] Target 	 86% Iranian + 0% Afghan_Pashtun + 5% Maasai + 9% Pathan @ D 	0.0139
[1] Target 	 86% Iranian + 5% Maasai + 9% Pathan + 0% Tadjik_Ishkashim @ D 	0.0139
[1] Target 	 86% Iranian + 5% Maasai + 9% Pathan + 0% Yamnaya @ D 	0.0139
[1] Target 	 86% Iranian + 5% Maasai + 9% Pathan + 0% Lezgin @ D 	0.0139
[1] Target 	 86% Iranian + 5% Maasai + 9% Pathan + 0% South_Italian @ D 	0.0139
[1] Target 	 86% Iranian + 5% Maasai + 9% Pathan + 0% Georgian_Laz @ D 	0.0139
[1] Target 	 0% Kurdish + 85% Iranian + 10% Afghan_Pashtun + 4.99999999999999% Maasai @ D 	0.0168
[1] Target 	 0% Azeri + 85% Iranian + 10% Afghan_Pashtun + 4.99999999999999% Maasai @ D 	0.0168
[1] Target 	 85% Iranian + 10% Afghan_Pashtun + 4.99999999999999% Maasai + 0% Tadjik_Ishkashim @ D 	0.0168
[1] Target 	 85% Iranian + 10% Afghan_Pashtun + 4.99999999999999% Maasai + 0% Druze @ D 	0.0168
[1] Target 	 85% Iranian + 10% Afghan_Pashtun + 4.99999999999999% Maasai + 0% Lebanese_Muslim @ D 	0.0168
[1] Target 	 85% Iranian + 10% Afghan_Pashtun + 4.99999999999999% Maasai + 0% Yamnaya @ D 	0.0168
[1] Target 	 85% Iranian + 10% Afghan_Pashtun + 4.99999999999999% Maasai + 0% Lezgin @ D 	0.0168
[1] Target 	 85% Iranian + 10% Afghan_Pashtun + 4.99999999999999% Maasai + 0% South_Italian @ D 	0.0168
[1] Target 	 85% Iranian + 10% Afghan_Pashtun + 4.99999999999999% Maasai + 0% Georgian_Laz @ D 	0.0168
[1] Target 	 81% Kurdish + 6.99999999999999% Maasai + 5% Pathan + 6.99999999999999% South_Indian @ D 	0.0179
[1] Target 	 83% Kurdish + 0% Azeri + 6.99999999999999% Maasai + 10% South_Indian @ D 	0.0185
[1] Target 	 83% Kurdish + 0% Afghan_Pashtun + 6.99999999999999% Maasai + 10% South_Indian @ D 	0.0185
[1] Target 	 83% Kurdish + 6.99999999999999% Maasai + 0% Tadjik_Ishkashim + 10% South_Indian @ D 	0.0185
[1] Target 	 83% Kurdish + 6.99999999999999% Maasai + 0% Druze + 10% South_Indian @ D 	0.0185
[1] Target 	 83% Kurdish + 6.99999999999999% Maasai + 0% Lebanese_Muslim + 10% South_Indian @ D 	0.0185
[1] Target 	 83% Kurdish + 6.99999999999999% Maasai + 0% Yamnaya + 10% South_Indian @ D 	0.0185
[1] Target 	 83% Kurdish + 6.99999999999999% Maasai + 0% Lezgin + 10% South_Indian @ D 	0.0185
[1] Target 	 83% Kurdish + 6.99999999999999% Maasai + 0% South_Italian + 10% South_Indian @ D 	0.0185
[1] Target 	 83% Kurdish + 6.99999999999999% Maasai + 10% South_Indian + 0% Georgian_Laz @ D 	0.0185
[1] Target 	 0% Kurdish + 87% Iranian + 5% Maasai + 8% Tadjik_Ishkashim @ D 	0.0188
[1] Target 	 0% Azeri + 87% Iranian + 5% Maasai + 8% Tadjik_Ishkashim @ D 	0.0188
[1] Target 	 87% Iranian + 5% Maasai + 8% Tadjik_Ishkashim + 0% Druze @ D 	0.0188
[1] Target 	 87% Iranian + 5% Maasai + 8% Tadjik_Ishkashim + 0% Lebanese_Muslim @ D 	0.0188
[1] Target 	 87% Iranian + 5% Maasai + 8% Tadjik_Ishkashim + 0% Yamnaya @ D 	0.0188
[1] Target 	 87% Iranian + 5% Maasai + 8% Tadjik_Ishkashim + 0% Lezgin @ D 	0.0188
[1] Target 	 87% Iranian + 5% Maasai + 8% Tadjik_Ishkashim + 0% South_Italian @ D 	0.0188
[1] Target 	 87% Iranian + 5% Maasai + 8% Tadjik_Ishkashim + 0% Georgian_Laz @ D 	0.0188
[1] Target 	 62% Kurdish + 7.00000000000001% Maasai + 20% Pathan + 11% Druze @ D 	0.0202
[1] Target 	 7% Maasai + 13% Pathan + 9% South_Indian + 71% Georgian_Laz @ D 	0.0206
[1] Target 	 78% Kurdish + 0% Azeri + 8% Maasai + 14% Pathan @ D 	0.021
[1] Target 	 78% Kurdish + 0% Afghan_Pashtun + 8% Maasai + 14% Pathan @ D 	0.021
[1] Target 	 78% Kurdish + 8% Maasai + 14% Pathan + 0% Tadjik_Ishkashim @ D 	0.021
[1] Target 	 70% Kurdish + 6.99999999999999% Maasai + 17% Pathan + 5.99999999999999% Lebanese_Muslim @ D 	0.021
[1] Target 	 78% Kurdish + 8% Maasai + 14% Pathan + 0% Yamnaya @ D 	0.021
[1] Target 	 78% Kurdish + 8% Maasai + 14% Pathan + 0% Lezgin @ D 	0.021
[1] Target 	 78% Kurdish + 8% Maasai + 14% Pathan + 0% South_Italian @ D 	0.021
[1] Target 	 78% Kurdish + 8% Maasai + 14% Pathan + 0% Georgian_Laz @ D 	0.021
[1] Target 	 7% Maasai + 29% Pathan + 16% Druze + 48% Georgian_Laz @ D 	0.0223
[1] Target 	 7% Maasai + 27% Pathan + 12% Lebanese_Muslim + 54% Georgian_Laz @ D 	0.0238
[1] Target 	 90% Iranian + 6.00000000000001% Maasai + 1.99999999999999% Yamnaya + 2% Lezgin @ D 	0.0241
[1] Target 	 0% Kurdish + 92% Iranian + 5.99999999999999% Maasai + 2% Yamnaya @ D 	0.0243
[1] Target 	 0% Azeri + 92% Iranian + 5.99999999999999% Maasai + 2% Yamnaya @ D 	0.0243
[1] Target 	 92% Iranian + 5.99999999999999% Maasai + 0% Druze + 2% Yamnaya @ D 	0.0243
[1] Target 	 92% Iranian + 5.99999999999999% Maasai + 0% Lebanese_Muslim + 2% Yamnaya @ D 	0.0243
[1] Target 	 92% Iranian + 5.99999999999999% Maasai + 2% Yamnaya + 0% South_Italian @ D 	0.0243
[1] Target 	 92% Iranian + 5.99999999999999% Maasai + 2% Yamnaya + 0% Georgian_Laz @ D 	0.0243
[1] Target 	 0% Kurdish + 85% Iranian + 6.00000000000001% Maasai + 9% Lezgin @ D 	0.0244
[1] Target 	 0% Azeri + 85% Iranian + 6.00000000000001% Maasai + 9% Lezgin @ D 	0.0244
[1] Target 	 85% Iranian + 6.00000000000001% Maasai + 0% Druze + 9% Lezgin @ D 	0.0244
[1] Target 	 85% Iranian + 6.00000000000001% Maasai + 0% Lebanese_Muslim + 9% Lezgin @ D 	0.0244
[1] Target 	 85% Iranian + 6.00000000000001% Maasai + 9% Lezgin + 0% South_Italian @ D 	0.0244
[1] Target 	 85% Iranian + 6.00000000000001% Maasai + 9% Lezgin + 0% Georgian_Laz @ D 	0.0244
[1] Target 	 0% Azeri + 7% Maasai + 17% South_Indian + 76% Georgian_Laz @ D 	0.0245
[1] Target 	 1% Afghan_Pashtun + 7% Maasai + 17% South_Indian + 75% Georgian_Laz @ D 	0.0245
[1] Target 	 7% Maasai + 0% Tadjik_Ishkashim + 17% South_Indian + 76% Georgian_Laz @ D 	0.0245
[1] Target 	 7% Maasai + 0% Druze + 17% South_Indian + 76% Georgian_Laz @ D 	0.0245
[1] Target 	 7% Maasai + 0% Lebanese_Muslim + 17% South_Indian + 76% Georgian_Laz @ D 	0.0245
[1] Target 	 7% Maasai + 0% Yamnaya + 17% South_Indian + 76% Georgian_Laz @ D 	0.0245
[1] Target 	 7% Maasai + 0% Lezgin + 17% South_Indian + 76% Georgian_Laz @ D 	0.0245
[1] Target 	 7% Maasai + 0% South_Italian + 17% South_Indian + 76% Georgian_Laz @ D 	0.0245
[1] Target 	 0% Azeri + 8% Maasai + 25% Pathan + 67% Georgian_Laz @ D 	0.0248
[1] Target 	 0% Afghan_Pashtun + 8% Maasai + 25% Pathan + 67% Georgian_Laz @ D 	0.0248
[1] Target 	 8% Maasai + 25% Pathan + 0% Tadjik_Ishkashim + 67% Georgian_Laz @ D 	0.0248
[1] Target 	 8% Maasai + 25% Pathan + 0% Yamnaya + 67% Georgian_Laz @ D 	0.0248
[1] Target 	 8% Maasai + 25% Pathan + 0% Lezgin + 67% Georgian_Laz @ D 	0.0248
[1] Target 	 8% Maasai + 25% Pathan + 0% South_Italian + 67% Georgian_Laz @ D 	0.0248
[1] Target 	 77% Kurdish + 0% Azeri + 15% Afghan_Pashtun + 8% Maasai @ D 	0.0267
[1] Target 	 77% Kurdish + 15% Afghan_Pashtun + 8% Maasai + 0% Tadjik_Ishkashim @ D 	0.0267
[1] Target 	 77% Kurdish + 15% Afghan_Pashtun + 8% Maasai + 0% Druze @ D 	0.0267
[1] Target 	 77% Kurdish + 15% Afghan_Pashtun + 8% Maasai + 0% Lebanese_Muslim @ D 	0.0267
[1] Target 	 77% Kurdish + 15% Afghan_Pashtun + 8% Maasai + 0% Yamnaya @ D 	0.0267
[1] Target 	 77% Kurdish + 15% Afghan_Pashtun + 8% Maasai + 0% Lezgin @ D 	0.0267
[1] Target 	 77% Kurdish + 15% Afghan_Pashtun + 8% Maasai + 0% South_Italian @ D 	0.0267
[1] Target 	 77% Kurdish + 15% Afghan_Pashtun + 8% Maasai + 0% Georgian_Laz @ D 	0.0267
[1] Target 	 0% Kurdish + 0% Azeri + 94% Iranian + 5.99999999999999% Maasai @ D 	0.0281
[1] Target 	 0% Kurdish + 94% Iranian + 5.99999999999999% Maasai + 0% Druze @ D 	0.0281
[1] Target 	 0% Kurdish + 94% Iranian + 5.99999999999999% Maasai + 0% Lebanese_Muslim @ D 	0.0281
[1] Target 	 0% Kurdish + 94% Iranian + 5.99999999999999% Maasai + 0% South_Italian @ D 	0.0281
[1] Target 	 0% Kurdish + 94% Iranian + 5.99999999999999% Maasai + 0% Georgian_Laz @ D 	0.0281
[1] Target 	 0% Azeri + 94% Iranian + 5.99999999999999% Maasai + 0% Druze @ D 	0.0281
[1] Target 	 0% Azeri + 94% Iranian + 5.99999999999999% Maasai + 0% Lebanese_Muslim @ D 	0.0281
[1] Target 	 0% Azeri + 94% Iranian + 5.99999999999999% Maasai + 0% South_Italian @ D 	0.0281
[1] Target 	 0% Azeri + 94% Iranian + 5.99999999999999% Maasai + 0% Georgian_Laz @ D 	0.0281
[1] Target 	 94% Iranian + 5.99999999999999% Maasai + 0% Druze + 0% Lebanese_Muslim @ D 	0.0281
[1] Target 	 94% Iranian + 5.99999999999999% Maasai + 0% Druze + 0% South_Italian @ D 	0.0281
[1] Target 	 94% Iranian + 5.99999999999999% Maasai + 0% Druze + 0% Georgian_Laz @ D 	0.0281
[1] Target 	 94% Iranian + 5.99999999999999% Maasai + 0% Lebanese_Muslim + 0% South_Italian @ D 	0.0281
[1] Target 	 94% Iranian + 5.99999999999999% Maasai + 0% Lebanese_Muslim + 0% Georgian_Laz @ D 	0.0281
[1] Target 	 94% Iranian + 5.99999999999999% Maasai + 0% South_Italian + 0% Georgian_Laz @ D 	0.0281
[1] Target 	 0% Azeri + 4% Maasai + 41% Pathan + 55% Druze @ D 	0.0294
[1] Target 	 0% Afghan_Pashtun + 4% Maasai + 41% Pathan + 55% Druze @ D 	0.0294
[1] Target 	 4% Maasai + 41% Pathan + 0% Tadjik_Ishkashim + 55% Druze @ D 	0.0294
[1] Target 	 4% Maasai + 41% Pathan + 55% Druze + 0% Lebanese_Muslim @ D 	0.0294
[1] Target 	 4% Maasai + 41% Pathan + 55% Druze + 0% Yamnaya @ D 	0.0294
[1] Target 	 4% Maasai + 41% Pathan + 55% Druze + 0% Lezgin @ D 	0.0294
[1] Target 	 4% Maasai + 41% Pathan + 55% Druze + 0% South_Italian @ D 	0.0294
[1] Target 	 4% Maasai + 41% Pathan + 55% Druze + 0% South_Indian @ D 	0.0294
[1] Target 	 80% Kurdish + 0% Azeri + 8% Maasai + 12% Tadjik_Ishkashim @ D 	0.0323
[1] Target 	 80% Kurdish + 8% Maasai + 12% Tadjik_Ishkashim + 0% Druze @ D 	0.0323
[1] Target 	 80% Kurdish + 8% Maasai + 12% Tadjik_Ishkashim + 0% Lebanese_Muslim @ D 	0.0323
[1] Target 	 80% Kurdish + 8% Maasai + 12% Tadjik_Ishkashim + 0% Yamnaya @ D 	0.0323
[1] Target 	 80% Kurdish + 8% Maasai + 12% Tadjik_Ishkashim + 0% Lezgin @ D 	0.0323
[1] Target 	 80% Kurdish + 8% Maasai + 12% Tadjik_Ishkashim + 0% South_Italian @ D 	0.0323
[1] Target 	 80% Kurdish + 8% Maasai + 12% Tadjik_Ishkashim + 0% Georgian_Laz @ D 	0.0323
[1] Target 	 0% Azeri + 3% Maasai + 38% Pathan + 59% Lebanese_Muslim @ D 	0.0331
[1] Target 	 0% Afghan_Pashtun + 3% Maasai + 38% Pathan + 59% Lebanese_Muslim @ D 	0.0331
[1] Target 	 3% Maasai + 38% Pathan + 0% Tadjik_Ishkashim + 59% Lebanese_Muslim @ D 	0.0331
[1] Target 	 3% Maasai + 38% Pathan + 59% Lebanese_Muslim + 0% Yamnaya @ D 	0.0331
[1] Target 	 3% Maasai + 38% Pathan + 59% Lebanese_Muslim + 0% Lezgin @ D 	0.0331
[1] Target 	 3% Maasai + 38% Pathan + 59% Lebanese_Muslim + 0% South_Italian @ D 	0.0331
[1] Target 	 3% Maasai + 38% Pathan + 59% Lebanese_Muslim + 0% South_Indian @ D 	0.0331
[1] Target 	 65% Iranian + 4% Pathan + 19% Lebanese_Muslim + 12% South_Indian @ D 	0.0343
[1] Target 	 0% Kurdish + 70% Iranian + 16% Lebanese_Muslim + 14% South_Indian @ D 	0.0344
[1] Target 	 0% Azeri + 70% Iranian + 16% Lebanese_Muslim + 14% South_Indian @ D 	0.0344
[1] Target 	 0% Azeri + 26% Afghan_Pashtun + 8% Maasai + 66% Georgian_Laz @ D 	0.0344
[1] Target 	 70% Iranian + 0% Afghan_Pashtun + 16% Lebanese_Muslim + 14% South_Indian @ D 	0.0344
[1] Target 	 70% Iranian + 0% Tadjik_Ishkashim + 16% Lebanese_Muslim + 14% South_Indian @ D 	0.0344
[1] Target 	 70% Iranian + 0% Druze + 16% Lebanese_Muslim + 14% South_Indian @ D 	0.0344
[1] Target 	 70% Iranian + 16% Lebanese_Muslim + 0% Yamnaya + 14% South_Indian @ D 	0.0344
[1] Target 	 70% Iranian + 16% Lebanese_Muslim + 0% Lezgin + 14% South_Indian @ D 	0.0344
[1] Target 	 70% Iranian + 16% Lebanese_Muslim + 0% South_Italian + 14% South_Indian @ D 	0.0344
[1] Target 	 70% Iranian + 16% Lebanese_Muslim + 14% South_Indian + 0% Georgian_Laz @ D 	0.0344
[1] Target 	 26% Afghan_Pashtun + 8% Maasai + 0% Tadjik_Ishkashim + 66% Georgian_Laz @ D 	0.0344
[1] Target 	 26% Afghan_Pashtun + 8% Maasai + 0% Druze + 66% Georgian_Laz @ D 	0.0344
[1] Target 	 26% Afghan_Pashtun + 8% Maasai + 0% Lebanese_Muslim + 66% Georgian_Laz @ D 	0.0344
[1] Target 	 26% Afghan_Pashtun + 8% Maasai + 0% Yamnaya + 66% Georgian_Laz @ D 	0.0344
[1] Target 	 26% Afghan_Pashtun + 8% Maasai + 0% Lezgin + 66% Georgian_Laz @ D 	0.0344
[1] Target 	 26% Afghan_Pashtun + 8% Maasai + 0% South_Italian + 66% Georgian_Laz @ D 	0.0344
    Last edited by jesus; 05-17-2015 at 02:53 AM.
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  6. 05-17-2015, 02:51 AM #534
    Kurd
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    I was curious about the 0s I was seeing in the oracle results, so I opened up the file 4mix.r to check the script. The combinations & permutations involve 3 pops with the 4th pop receiving an assignment of 1-(pop1+pop2+pop3)). I tried to re-write the script but failed. Maybe someone more talented in R programming can look into it.
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  7. 05-17-2015, 02:59 AM #535
    Krefter
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    Germany Imperial United Kingdom Norway Spain

    Can someone teach me how to use "sink"?
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  8. 05-17-2015, 03:02 AM #536
    surbakhunWeesste
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    Quote Originally Posted by Kurd View Post
    I was curious, did you have to add the above command to run your file. The reason being is that in R that command is an instruction to create a file called tVec from your results file (target) which appears to be not comma separated (likely tab)

    Zephs problem is probably with his Eurogenes spreadsheet having duplicate pop labels
    nah! just source('4mix.r') followed by the Day tripper's code

    Quote Originally Posted by Kurd View Post
    I was curious about the 0s I was seeing in the oracle results, so I opened up the file 4mix.r to check the script. The combinations & permutations involve 3 pops with the 4th pop receiving an assignment of 1-(pop1+pop2+pop3)). I tried to re-write the script but failed. Maybe someone more talented in R programming can look into it.
    I am not even complaining. There can be an issue with run time but it works well. A different algorithm can create a whole different result. I am still early on understanding how they have been separating alleles to designate populations like the ANE & SSA stuff tbh.
    I did rewrite the code and was able to generate 2 iterations with many warnings and errors. So, I just followed Day tripper's for loop

    If you wanna run it in OSX you will need XQuartz to support it as well.
    Last edited by surbakhunWeesste; 05-17-2015 at 04:51 AM.
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  10. 05-17-2015, 03:10 AM #537
    surbakhunWeesste
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    Quote Originally Posted by Krefter View Post
    Can someone teach me how to use "sink"?

    Pre Reqs.
    K8avg.csv, target.txt, 4mix.r file all in one folder(directory)


    1. Click/double click on the 4mix.r file >it will open your R console
    2. Type/paste in source('4mix.r')
    3.Type/Paste in
    Code:
    sink("sink.txt")
poplist <- (c("Kurdish","Azeri","Iranian","Afghan_Pashtun","Maasai","Pathan","Tadjik_Ishkashim","Druze","Lebanese_Muslim","Yamnaya","Lezgin","South_Italian","South_Indian","Georgian_Laz"))

for (i in 1:11)
	for (j in (i + 1):12)
		for (k in (j + 1):13)
			for (l in (k + 1):14)
getMix('K8avg.csv','target.txt',poplist[i],poplist[j],poplist[k],poplist[l])
    After ~10+ minutes if you check your folder a 'sink.txt' will be generated with target populations. To sort it copy paste it on excel and sort.

    screen shot
    Attachment 4603
    Last edited by surbakhunWeesste; 05-17-2015 at 03:24 AM.
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  12. 05-17-2015, 03:21 AM #538
    Kurd
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    Quote Originally Posted by zahra View Post
    nah! just source('4mix.r') followed by the Day tripper's code



    I am not even complaining. There is an issue with run time as well but it works. A different algorithm can create a whole different result. I am still early on understanding how they have been separating alleles to designate a population like the ANE & SSA stuff tbh.

    If you wanna run it in OSX you will need XQuartz to support it as well.
    Ok thanks, I was trying to figure out how
    tVec <- read.table(file = target, head = TRUE, sep = "\t", row.names = 1
    )fit into this picture.

    There is nothing that can be done about the time consuming issue because of the number of combinations and permutations, unless you want to delete the irrelevant pops in the spreadsheet, and use less pops in the set Pop(1).....pop(n)
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  14. 05-17-2015, 04:10 AM #539
    Krefter
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    Quote Originally Posted by zahra View Post
    Pre Reqs.
    K8avg.csv, target.txt, 4mix.r file all in one folder(directory)


    1. Click/double click on the 4mix.r file >it will open your R console
    2. Type/paste in source('4mix.r')
    3.Type/Paste in
    Code:
    sink("sink.txt")
poplist <- (c("Kurdish","Azeri","Iranian","Afghan_Pashtun","Maasai","Pathan","Tadjik_Ishkashim","Druze","Lebanese_Muslim","Yamnaya","Lezgin","South_Italian","South_Indian","Georgian_Laz"))

for (i in 1:11)
	for (j in (i + 1):12)
		for (k in (j + 1):13)
			for (l in (k + 1):14)
getMix('K8avg.csv','target.txt',poplist[i],poplist[j],poplist[k],poplist[l])
    After ~10+ minutes if you check your folder a 'sink.txt' will be generated with target populations. To sort it copy paste it on excel and sort.

    screen shot
    Attachment 4603
    Thanks alot! This saves alot of time.
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  16. 05-17-2015, 05:44 AM #540
    Kurd
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    I was able to get the outsourcing to sink folder method to work with other calculator spreadsheets. Here are mine for the WEAC2 spreadsheet. I was able to get down to a distance of 0.0131 with a 3 population mix.

    [IMG][/IMG]
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