Eurogenes Biogeographic Ancestry Project

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09-15-2011, 03:44 PM
Humanophage

Removed NE-E and Volga to break down my East European score:
West_Euro + 45.6
West_Asian + 18.8
South_Asian + 5.8
East_Med + 3.2
East_Siberian + 3.0
Mid_East + 2.8
South_Siberian + 2.2
North_Asian + 1.6

Code:

no NE-E, no Volga no NE-E full 0.00% Sub-Saharan 5.30% Sub-Saharan 0.00% Sub-Saharan 0.00% North_African 0.06% North_African 0.00% North_African 5.98% South_Asian 3.15% South_Asian 0.04% South_Asian 57.43% West_Euro 45.27% West_Euro 11.85% West_Euro 0.00% Southeast_Asian 1.43% Southeast_Asian 0.00% Southeast_Asian 2.22% South_Siberian 0.05% South_Siberian 0.00% South_Siberian 1.59% North_Asian 0.01% North_Asian 0.00% North_Asian 3.02% East_Siberian 1.21% East_Siberian 0.00% East_Siberian 0.00% East_Asian 0.12% East_Asian 0.00% East_Asian 5.63% East_Mediter 3.53% East_Mediter 2.45% East_Mediter 4.63% Middle_Eastern 3.65% Middle_Eastern 1.82% Middle_Eastern 19.49% West_Asian 14.42% West_Asian 0.72% West_Asian 21.81% Volga-Ural 82.35% Northeast_Euro 0.77% Volga-Ural

Quote:

Originally Posted by Imperivm

Sorry chaps, I'm using a mac as my main computer and it's not letting me run the Dodecad DIY without giving me errors (I think it's because of the type of mac OS I'm running). If you don't need the raw data file for this (I assume you don't); could somebody run the tests for me, please? I'm UK35.

One needs the raw data file for this. The whole thing is fairly fundamental.
09-15-2011, 05:18 PM
Rochefaton

Me:
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

30.86% Northeast_Euro
0.00% Sub-Saharan
0.23% N. African
0.95% South_Asian
57.53% West_Euro
0.00% Southeast_Asian
0.05% South_Siberian
0.00% North_Asian
0.00% East_Siberian
0.00% East_Asian
2.32% East_Mediterranean
0.67% Middle_Eastern
5.43% West_Asian
1.96% Volga-Ural

My Wife:
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

28.96% Northeast_Euro
0.80% Sub-Saharan
0.00% N. African
0.01% South_Asian
57.25% West_Euro
0.02% Southeast_Asian
0.00% South_Siberian
0.05% North_Asian
0.99% East_Siberian
0.00% East_Asian
4.65% East_Mediterranean
1.85%% Middle_Eastern
4.44% West_Asian
0.99% Volga-Ural
09-15-2011, 05:27 PM
poiuytrewq0987

Whenever I try to open the Dodecad exe, a command window opens but it immediately closes after opening. What am I doing wrong? :rolleyes:
09-15-2011, 07:28 PM
Frederick

Quote:

Originally Posted by Dušan

Whenever I try to open the Dodecad exe, a command window opens but it immediately closes after opening. What am I doing wrong? :rolleyes:

You need to have "R" installed.
And then you open the "R" exe.

Seems like you never did this before, so you need to "standarize" your genomefile first.

Here are some selected lines from the "Read Me":

Quote:

2. Download and install R (http://www.r-project.org/) if you haven't done so
already.

Quote:

3. Download and unzip your genotype data file from 23andMe or FamilyTreeDNA
into the working directory (The directory with the DiY stuff and files in). This should be a file ending in .txt for 23andMe
and .csv for
FamilyTreeDNA.

From now on, I will suppose that your genotype file is named 'johndoe.txt' or
'johndoe.csv'

4. Launch R.

Quote:

Once R is running, it will give you a command prompt where you can enter
commands. First, you must change the directory to your working directory.

You can do this from the File -> Change dir menu in Windows

Quote:

Then, enter:

source('standardize.r')

This loads a small program that will convert your data from the
company-specific format to a common format in the next step.

5. At the R prompt, enter:

a. If you have 23andMe data (either v2 or v3 chip):

standardize('johndoe.txt', company='23andMe')

Then your genomefile is "stardarized", wich you will need for all other experiments you ever do with DIY.

And then you type system('DIYDodecadWin test.par') to run it with this latest Eurogenes run. (make sure you downloaded this https://docs.google.com/viewer?a=v&p...iYTJh&hl=en_US and extract it into the "Working directory)

This line instead: system('DIYDodecadWin dv3.par') would run your Dodecad results btw.
09-15-2011, 08:56 PM
Barreldriver

Bah, I have not winrar to unpack the .rar's for the initial DIY programs or the patience to mess around with 'em. :(
09-15-2011, 09:53 PM
Scrapple

Quote:

Originally Posted by Barreldriver

Bah, I have not winrar to unpack the .rar's for the initial DIY programs or the patience to mess around with 'em. :(

http://www.7-zip.org/ will work on .rar files.
09-15-2011, 10:35 PM
Damião de Góis

65.04% West_Euro
13.71% Northeast_Euro
11.51% East_Mediterranean
5.36% Middle_Eastern
2.03% Berber
1.84% Sub-Saharan
0.28% Southeast_Asian
0.23% West_Asian

0.00% South_Asian
0.00% South_Siberian
0.00% North_Asian
0.00% East_Siberian
0.00% East_Asian
0.00% Volga-Ural
09-15-2011, 11:09 PM
Barreldriver

Quote:

Originally Posted by Commerce & Industry

http://www.7-zip.org/ will work on .rar files.

Completely forgot about this used to have much of these sorts of things on my laptop but I had a number of foul ups resulting in a restore to factory default. :P

Will post my results once I get all this stuff reinstalled and organized.
09-15-2011, 11:21 PM
Aviane

Quote:

Originally Posted by Frederick

That map has a huge overlap of Germany, Lower Countries, Kent and an undefined part of France.

I guess Johnston can keep his dream of West-Germanic unity. ;)

http://www.theapricity.com/forum/att...1&d=1315320704

I agree with this the countries mentioned cluster altogether.

Quote:

Originally Posted by Barreldriver

Completely forgot about this used to have much of these sorts of things on my laptop but I had a number of foul ups resulting in a restore to factory default. :P

Will post my results once I get all this stuff reinstalled and organized.

It's good to hear from you as being another member.
09-15-2011, 11:49 PM
Barreldriver

I must be retarded as I cannot get R to work and thus cannot run the DIY or the Eurogenes add ons. :P Still stuck at the standardize.r phase. :(

EDIT:

nvm, found I had the wrong directory selected. bwahaha

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