Eurogenes Biogeographic Ancestry Project

[Oneeye]

From the readme:



Then the command to start the actual analysis is:

system('DIYDodecadWin admix.par')

When I try to standardize my genome file, I get:

"Error in is.data.frame(x) : object 'X' not found"

.....?

[Mark]

Make sure you have 'admix.par' in the working directory.
Or, have you alternately used a DOS prompt with the 'DIYDodecadWin dv3.par' command?

[Oneeye]

Make sure you have 'admix.par' in the working directory.
Or, have you alternately used a DOS prompt with the 'DIYDodecadWin dv3.par' command?

I do have admix.par in the working directory.

I'm trying to "standardize" my genome in R before starting up DIYDodeocad, sorry about how the quote turned out. I'm right here at the bolded part:

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, or by using the
setwd command in either Windows or Linux, e.g.:

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')

[Mark]

Okay, did you change/rename the 23andme .txt file. If so, that may be the issue.
Edit: Or rather, change the command to reflect YOURNAME.txt if you haven't already.

[Atlantic Islander]

When I try to standardize my genome file, I get:

"Error in is.data.frame(x) : object 'X' not found"

.....?

I have the commands saved in notepad, I just copy paste the whole thing into R:

source('standardize.r')
standardize('yourfilenamehere.txt', company='23andMe')
system('DIYDodecadWin admix.par')

You have to make sure you do this first: open R and go to file > change dir... > C: > Program files > DIYdodecad 2.1 and click ok.

[Maleficent]

Eurogenes K36(old)
19.10% East_Mediterranean
10.27% French
9.74% Italian
9.67% Near_Eastern
8.37% North_Atlantic
7.41% Iberian
6.77% North_Sea
5.79% Arabian
5.47% Armenian
3.77% Central_European
3.39% Mediterranean
2.23% East_Balkan
1.63% North_Caucasian
1.50% North_African
1.43% West_Mediterranean
0.97% South_Central_Asian
0.67% Eastern_European
0.57% Northeast_African
0.54% Basque
0.52% West_Caucasian
0.12% Finnish
0.06% East_African
0.01% East_Central_European

Eurogenes K36(new)
16.23% East_Med
13.20% Near_Eastern
11.64% Italian
10.04% French
9.28% Iberian
7.34% North_Sea
6.49% North_Atlantic
6.47% Arabian
4.55% Armenian
4.32% North_Caucasian
2.56% East_Balkan
2.40% Central_Euro
1.66% West_Med
1.24% South_Central_Asian
0.95% North_African
0.35% Fennoscandian
0.35% East_African
0.33% Eastern_Euro
0.30% West_African
0.15% Basque
0.10% Northeast African
0.07% West_Caucasian

[Oneeye]

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

0.19% Amerindian
0.00% Arabian
1.24% Armenian
1.01% Basque
0.00% Central_African
6.90% Central_European
0.00% East_African
0.00% East_Asian
3.92% East_Balkan
0.00% East_Central_Asian
3.20% East_Central_Europea
0.00% East_Mediterranean
5.02% Eastern_European
13.33% Finnish
8.76% French
16.78% Iberian
0.00% Indo-Chinese
4.14% Italian
0.00% Malayan
2.53% Mediterranean
0.00% Near_Eastern
0.00% North_African
12.51% North_Atlantic
2.74% North_Caucasian
17.45% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.03% South_Central_Asian
0.00% South_Chinese
0.04% Volga-Ural
0.00% West_African
0.00% West_Caucasian
0.21% West_Mediterranean

CPU time = 2109.00 sec

[Oneeye]

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

20.60% North_Sea
17.07% Iberian
12.30% Fennoscandian
11.91% North_Atlantic
7.76% French
7.40% Italian
5.87% Central_Euro
3.84% East_Balkan
3.51% Eastern_Euro
3.27% East_Central_Euro
3.17% North_Caucasian
1.28% Basque
1.21% Armenian
0.34% South_Central_Asian
0.26% Amerindian
0.12% West_Med

CPU time = 1634.91 sec
>

[Graham]

I like this, but Sardinians were used for the West_Med component. Since you have a South-East Europe category, I think there should be a South-West Europe category as well. Just a suggestion.

Added West Med & made a South West Table here.
South West Europe --Basque, Iberian, Italian & West Med
54.37% -- Kadu
53.35% -- Alex Delarge
------------------------------------
48.52% -- Atlantic Islander
41.80% -- Pappa Diddy Pop
37.06% -- Sicilianu101
36.69% -- Loki
33.29% -- Alpine Celt
31.47% -- Otto Prohaska Mum
31.04% -- Mark
------------------------------------
25.87% -- Oneeye
25.57% -- Otto Prohaska
25.50% -- Jackson Dad
23.49% -- Jackson Grandad
22.73% -- FairyPrincess
21.23% -- Graham
20.96% -- Sgc2009 Gran
20.58% -- Jackson
------------------------------------
19.21% -- Xyresic
18.76% -- Equilibrium
17.92% -- Evon Gran
17.73% -- Evon
17.01% -- Evon Uncle
16.93% -- Otto Prohaska Dad
16.02% -- Evon Aunt
13.17% -- Partizan
11.96% -- Kazimiera
10.64% -- Jockman
10.54% -- Drogin Dad
------------------------------------
09.60% -- Orangepulp Aunt
08.64% -- Drogin
07.69% -- Orangepulp
06.39% -- Jockman Grandad
06.14% -- Pallantides
02.70% -- Polako

[Graham]

North West Europe -- North Atlantic & North Sea
39.55% -- Graham
39.34% -- Pallantides
36.88% -- Evon
36.58% -- Evon Uncle
35.70% -- Evon Aunt
35.62% -- Jackson Grandad
35.45% -- Jackson
35.08% -- Jackson Dad
33.88% -- Drogin
33.40% -- Sgc2009 Gran
32.51% -- Oneeye
31.75% -- Evon Gran
30.24% -- Kazimiera
------------------------------------
29.25% -- Otto Prohaska Mum
26.71% -- Jockman
25.01% -- Loki
24.70% -- Drogin Dad
22.99% -- Otto Prohaska Dad
21.82% -- Jockman Grandad
21.11% -- Otto Prohaska
20.25% -- Pappa Diddy Pop
19.75% -- Atlantic Islander
19.21% -- Polako
18.02% -- Kadu
17.37% -- Alpine Celt
13.83% -- FairyPrincess
13.71% -- Alex Delarge
------------------------------------
05.78% -- Sicilianu101
04.98% -- Mark
01.23% -- Xyresic