Quote:
Originally Posted by Otto Prohaska
When I try to standardize my genome file, I get:
"Error in is.data.frame(x) : object 'X' not found"
.....?
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Quote:
Originally Posted by Otto Prohaska
When I try to standardize my genome file, I get:
"Error in is.data.frame(x) : object 'X' not found"
.....?
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.Quote:
Originally Posted by mark
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:
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, 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')
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.
I have the commands saved in notepad, I just copy paste the whole thing into R:Quote:
Originally Posted by Oneeye
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.
Eurogenes K36(new)Quote:
Originally Posted by FairyPrincess
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
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
----------------------------
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
>
Added West Med & made a South West Table here.Quote:
Originally Posted by Atlantic Islander
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
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
Quote:
Originally Posted by Graham
Fantastic, thanks. :)Quote:
Originally Posted by Graham
Ha, sorry, I forgot that it is possible to edit posts a long time after they are made.
Sorry, if you see any errors Rep me. Do it all manually & my brain becomes lazy, tired & bored. :P
----------------------------
K35 - FINAL ADMIXTURE PROPORTIONS:
----------------------------
16.27% East_Med
15.30% Near_Eastern
15.05% Italian
9.04% Iberian
6.46% Arabian
4.83% East_Central_Euro
4.82% West_Med
3.98% Central_Euro
3.96% Armenian
3.75% West_Caucasian
3.54% East_Balkan
2.91% North_Atlantic
2.65% North_African
2.29% North_Sea
2.14% Basque
1.55% French
0.62% Volga-Ural
0.26% North_Caucasian
0.40% Northeast_African
0.17% Eastern_Euro
0.00% Amerindian
0.00% Central_African
0.00% East_Central_Asian
0.00% East_African
0.00% East_Asian
0.00% Fennoscandian
0.00% Indo-Chinese
0.00% Malayan
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% West_African
> Link to K35 Files
K35 -
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------
26.42% Iberian
12.58% Italian
11.21% North_Sea
----------------------------
8.54% North_Atlantic
7.76% West_Med
6.55% French
5.14% Central_Euro
4.60% North_African
3.07% Arabian
2.71% East_Med
2.45% Fennoscandian
2.09% East_Balkan
1.97% Near_Eastern
1.76% Basque
1.55% Volga-Ural
1.28% Northeast_African
----------------------------
0.17% Omotic
0.11% East_Central_Euro
0.03% Oceanian
----------------------------
0.00% Amerindian
0.00% Armenian
0.00% Central_African
0.00% East_African
0.00% East_Asian
0.00% East_Central_Asian
0.00% Eastern_Euro
0.00% Indo-Chinese
0.00% Malayan
0.00% North_Caucasian
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% West_African
0.00% West_Caucasian
The same as before of course.
Seems the same as the last one. Probably a population where i scored 0% was dropped.
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------
0.00% Amerindian
0.46% Arabian
2.05% Armenian
4.56% Basque
0.00% Central_African
4.59% Central_Euro
0.00% East_African
0.00% East_Asian
0.01% East_Balkan
0.00% East_Central_Asian
6.09% East_Central_Euro
0.17% East_Med
0.00% Eastern_Euro
1.51% Fennoscandian
6.64% French
23.53% Iberian
0.00% Indo-Chinese
19.07% Italian
0.00% Malayan
2.63% Near_Eastern
5.31% North_African
7.97% North_Atlantic
1.92% North_Caucasian
5.74% North_Sea
0.00% Northeast_African
0.02% Oceanian
0.93% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% Volga-Ural
0.58% West_African
0.02% West_Caucasian
6.19% West_Med
This is K35 (K36 without the Fennoscandian component).
(+- %) = comparison with K36.
Me
17.93% Eastern_European (+8,5%)
15.92% North_Atlantic (+5,36%)
---------------------------
14.48% North_Sea (+1,67%)
11.34% Central_European (+5,66%)
11.33% East_Central_European (+5,43%)
---------------------------
6.92% East_Balkan (+0,66%)
5.92% Iberian (+1,89%)
---------------------------
3.98% French (+2,03%)
3.44% Italian (-0,68%)
2.95% Volga-Ural (+1,6%)
2.21% Basque (-0,16%)
1.55% Siberian (+1,53%)
1.06% Malayan (+0,48%)
---------------------------
0.27% East_Central_Asian (-0,28%)
0.26% South_Central_Asian (+0,2%)
0.19% Oceanian (-0,18%)
0.18% North_Caucasian (-1,66%)
0.03% South_Asian (+0,03%)
0.02% Indo-Chinese (-0,2%)
My grandpa
14.29% East_Central_European (+7,59%)
13.94% North_Sea (-0,66%)
13.40% Eastern_European (+8,95%)
13.12% North_Atlantic (+5,87%)
---------------------------
9.41% French (+3,27%)
9.06% Central_European (+5,17%)
7.62% Volga-Ural (+1,89%)
5.75% East_Balkan (+0,75%)
---------------------------
4.82% Siberian (+1,89%)
3.51% Iberian (+1,46%)
2.32% Basque (+0,72%)
1.40% Italian (-0,79%)
---------------------------
0.89% Amerindian (+0,29%)
0.27% Oceanian (+0,25%)
0.10% Pygmy (-0,21%)
0.08% Malayan (-0,38%)
0.01% North_Caucasian (0,03%)
0.01% Indo-Chinese (-0,01%)
0.01% East_Central_Asian (-0,02%)
It has giving you some Siberian like your Grandad.
Yea it was hidden there deep in the Fennoscandian component.Quote:
Originally Posted by Graham
me and my grandfather for comparison, with the components you have used earlier :)
http://s11.postimg.org/dtaasrneb/k35c.jpg
^^^
Like I said before, your Western European scores would be lower with a Swedish/Norwegian/Danish cluster.. It Would lower the North Sea & North Atlantic scores, for people like yourself. :) Can't happen though, until we have samples that aren't members.
Runs like Eurogenes, are only at baby steps, with far greater potential to build on.
Kadu edited the original k36 files to make a K28, so here are my results with his edited files:
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------
35.92% Iberian
11.41% North_Sea
10.80% North_Atlantic
----------------------------
9.37% West_Mediterranean
7.93% Central_European
5.73% East_Mediterranean
5.00% East_Balkan
4.57% North_African
2.96% Near_Eastern
2.64% Arabian
2.20% Volga-Ural
----------------------------
0.50% Northeast_African
0.43% Eastern_European
0.37% Central_African
0.16% Oceanian
----------------------------
0.00% Amerindian
0.00% East_African
0.00% East_Asian
0.00% East_Central_Asian
0.00% Indo-Chinese
0.00% Malayan
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% West_African
0.00% West_Caucasian
K35 FINAL ADMIXTURE PROPORTIONS:
16.76% East_Central_Euro
16.41% North_Sea
13.83% North_Atlantic
====================
8.87% Fennoscandian
8.31% Central_Euro
7.87% Eastern_Euro
7.05% Italian
5.23% French
3.45% Iberian
2.07% East_Balkan
2.05% West_African
1.68% South_Central_Asian
1.46% Basque
1.37% Volga-Ural
1.09% West_Caucasian
1.05% Oceanian
0.84% North_Caucasian
0.21% Central_African
0.15% Amerindian
0.12% East_Med
0.12% Omotic
0.01% Near_Eastern
0.01% East_African
0.00% Arabian
0.00% Armenian
0.00% East_Asian
0.00% East_Central_Asian
0.00% Indo-Chinese
0.00% Malayan
0.00% North_African
0.00% Northeast_African
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% West_Med
Chromosome 11, which contains quite a lot of SNPs.... Funny results, considering my norwegian/finnish heritage.
I guess this result is partly the reason why my north-caucasian component is so high genome-wide too
28.13% East_Central_Euro
21.84% Fennoscandian
13.93% North_Caucasian
13.59% North_Atlantic
10.15% French
5.08% West_Caucasian
3.72% North_Sea
3.51% Amerindian
0.03% Central_Euro
0.02% Eastern_Euro
------------------
0.00% Arabian
0.00% Armenian
0.00% Basque
0.00% Central_African
0.00% East_African
0.00% East_Asian
0.00% East_Balkan
0.00% East_Central_Asian
0.00% East_Med
0.00% Iberian
0.00% Indo-Chinese
0.00% Italian
0.00% Malayan
0.00% Near_Eastern
0.00% North_African
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% Volga-Ural
0.00% West_African
0.00% West_Med
I'm still trying to figure out where the locations for East-Central Euro, North Sea and North Atlantic is. Which countries??
East-central-euro is basicly ukrainians and south-west russiansQuote:
Originally Posted by Kazimiera
>> link to K36 - Reference PopulationsQuote:
Originally Posted by Kazimiera
I think Graham should know.Quote:
Originally Posted by Kazimiera
E-C-E should be mostly Polish I think, and North Sea would be parts of Scandinavia, Netherlands, north Germany ... essentially a Germanic thing. North Atlantic also overlaps of course with North Sea, NA being more to the west (Britain, Ireland).
Edit: someone was faster
North Sea is Kent, & North Atlantic is mainly Cornwall.
Kent -- North Sea
http://upload.wikimedia.org/wikipedi...p_2010.svg.png
Cornwall -- North Atlantic
http://upload.wikimedia.org/wikipedi...p_2010.svg.png
Yep, Germanic south-east and pre-Germanic Cornwall.Quote:
Originally Posted by Graham
I think he used Kent as the North Sea group and Argyll, CEU, Cornwall as North Atlantic, can't remember exactly.Quote:
Originally Posted by Loki
I don't think Kent is as Germanic as people think, at least not as much as East Anglia and parts of the East Midlands - They would have made a better reference group if there were available samples from there.Quote:
Originally Posted by Loki
I'm not sure, I think Kent is quite Germanic. We know that the Jutes settled there. Rural East Anglia doesn't tell much, influence should more show in the larger towns ... like for example Lincoln to the north.Quote:
Originally Posted by Jackson
How does the Y-DNA & mtDNA of Kent compare to others in England? If that information is available.
There should be maps somewhere with haplogroup distributions.Quote:
Originally Posted by Graham
True, although in England south of the Thames (and i guess basically in the home counties) R1b-P312 L21- U152- and R1b U152 are more common than in Anglia and East Midlands, and R1b is higher overall as well, than in East Anglia and the East Midlands. It's not a massive difference i agree with you there, it's still predominately Germanic but there seems to be a bit more of a Celtic remnant there than in a couple of other places. That could partly be due to it being outside the Danelaw, while East Anglia and the East Midlands was in the heart of the Danelaw.Quote:
Originally Posted by Loki
I disagree, in the bigger towns and in cities there tends to be more non-local ancestry, which in the case of the last few hundred years has been mainly from Ireland and western Britain. In fact POBI have shown that on average people from urban areas in a certain region (of England) tended to be more Celtic influenced than the people in the countryside around them. I don't know if the same is true in the Celtic fringe (that people from towns are less Celtic than in the surrounding countryside) but it could be, although to a much lesser degree in most areas.
Thats not saying that none moved to the country, but most went to cities and towns first it seems, a bit like our current wave of immigrants that start in the towns and then filter out a bit from there i suppose.
The most Germanic areas seem to be the Anglian peninsula and Lindsey (much of what is now Lincolnshire) then followed by the rest of the East Midlands and the South-East (including Kent).
Kent should be quite similar to the one in south/south-east England on this map. Edit: This is just R1b, but it does demonstrate it to some degree.Quote:
Originally Posted by Graham
http://i628.photobucket.com/albums/u...uropeBusby.jpg
This is interesting. I have travelled along the coast of East Anglia and stopped in every town. The locals in the small villages there look mainly stocky, swarthy etc ... the opposite of Germanic. But as I go into larger towns and cities, blonds seem to become more common. Just my personal observation.Quote:
Originally Posted by Jackson
All the Polish immigrants. :DQuote:
Originally Posted by Loki
That's an interesting observation. I can't counteract that in any way using equivalent observations so i'll just have to take your word for correct on this. Although i would say that looks and genetics don't always correlate.
Netherlands would make a better cluster than Kent..Cornwall is a good one.
Netherlands, East Anglia - Doggerland
Cornwall, Wales, Ireland - North Atlantic
East Norway, Sweden - Scandinavian
Finland - Finland