MDLP K17

Scroll to the bottom for instructions for other calculators.

I'll assume that you're using Windows, but refer to DIYDodecad's README.txt file if you're running Linux. I don't think there's Mac OS support for DIYDodecad, but you might have luck using Wine.

	Admixture:

1. Download and install R: http://www.r-project.org/
2. Download DIYDodecad: http://dodecad.blogspot.co.uk/2011/09/do-it-yourself-dodecad-v-21.html
3. Download the MDLP K17 package: https://drive.google.com/file/d/0B6n7iMc2P-yQaWhVWTZkczJtLUk/edit?usp=sharing
4. Download your 23andMe raw data file: https://www.23andme.com/you/download/
5. Extract and place the DIYDodecad, K17 & 23andMe files into the same folder.
6. Open R and change the directory (File > Change Dir) to the folder where you placed your DIY, K17 & raw data files.
7. Enter this command in R:
source('standardize.r')

8. Enter this command but replace X with the name of your raw data file:
standardize('X.txt', company='23andMe')

9. Enter this command:
system('DIYDodecadWin k17.par')

That's it. Just be patient, the results might take some time to generate.


	Oracle:

Once you've obtained your Admixture results, you can then calculate your Oracle results using the TOraclerelease.RData file and TOracle() function.

1. Open the 'TOraclerelease.RData' file in R (File > Load Workspace, or double-clicking the file should do it).
2. Enter this command but replace X with your Admixture results in sequence, separated by commas and excluding the percentage signs:
TOracle(c(X), k=20)

For example, my Admixture results are:

25.22% Caucasian-Basal
0.37% Melano-Austronesian
1.28% Uralic
0.41% Ancestral_East_Siberian
0.86% Ancestral_West_Siberian
21.64% Ancestral_North_Indian
0.73% Ancestral_South_Indian
4.75% West_European_HG
0.01% Ancestral_Sami-Finnic
0.78% South_East_Asian
0.57% Archaic_African
22.55% Ancestral_Mediterranean_EEF
1.06% Circumpolar
17.65% Near-East-Basal
0.01% Ancestral_East_European_ANE
1.55% African_Sub_Saharian
0.55% Amerindian

So I would type:

TOracle(c(25.22, 0.37, 1.28, 0.41, 0.86, 21.64, 0.73, 4.75, 0.01, 0.78, 0.57, 22.55, 1.06, 17.65, 0.01, 1.55, 0.55), k=20)

That gives you Single Population Sharing results.

3. For Mixed Mode Population Sharing, add 'mixedmode=T' to the command:

TOracle(c(X), k=20, mixedmode=T)

4. If you want greater or less than 20 results, change k=20 to k=X, where X is the number of results you want to generate.
For example:

TOracle(c(X), k=250, mixedmode=T)


	Using other MDLP, Dodecad, Eurogenes or Harappa calculators:

The same Admixture steps apply if you'd prefer to use a different calculator.
Follow the steps in the Admixture section above, but ignore step 3 and download your chosen calculator package instead.
In steps 5 & 6, "K17" refers to your chosen calculator.
In step 9, replace k17.par with X.par, where X is the name of the par file included in your chosen calculator package.

If an Oracle RData file is included with your chosen calculator package, the Oracle instructions above will work if used with the correct function.
The correct function differs with each calculator: MDLP K17 uses TOracle(), Dodecad K12b uses DodecadOracle() and HarappaWorld uses HarappaOracle()
If the function to use isn't included in a README file with the package or on the project's website, open the RData file in R as normal and type the following command to locate the function:
ls()


***Note:
In step 8 of the Admixture section above, the "standardize" function creates the file "genotype.txt". Keep this file and DIYDodecadWin.exe for future use.
The genotype.txt file allows you to skip a couple of steps and can be used for all DIY calculators released by MDLP, Dodecad, Eurogenes and Harappa projects.

1. Download your chosen calculator package and extract it.
2. Copy the genotype.txt file, DIYDodecadWin.exe file and the package contents of your chosen calculator into the same folder.
3. Open R and change the directory (File > Change Dir) to the folder where you placed your genotype.txt, DIYDodecadWin.exe and calculator files.
4. Enter this command but replace X with the name of the par file included with your chosen calculator:
system('DIYDodecadWin X.par')

That's it.