tag:blogger.com,1999:blog-4123559132014627431.post6480610627255694854..comments2024-03-28T08:39:32.244-07:00Comments on Eurogenes Blog: Haplotype-based PCA of West Eurasia and EuropeDavidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger23125tag:blogger.com,1999:blog-4123559132014627431.post-75873834373313260972019-09-12T01:52:20.920-07:002019-09-12T01:52:20.920-07:00About Time
They can not "came down" by...About Time <br /><br />They can not "came down" by the simple reason as the earliest mentioned Slavonia region is in the Balkans/Danube region/. The Russians were called slavs about 1000 years after the name Slavs / Sclaveni was registered in the lands of the Gets. natsunoamehttps://www.blogger.com/profile/07946553288506970769noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-6036786208950862562016-07-09T09:20:43.485-07:002016-07-09T09:20:43.485-07:00You need to first make sure that the output looks ...You need to first make sure that the output looks exactly like this in a fastIBD.txt file, with each segment shared by pairs of samples expressed as a cM score. I can't explain here how to do that. I'd need to write up a tutorial.<br /><br />Ecuadorian_GSM531168 Yoruban_HGDP00943 0.6925<br />Bantu_S.E._HGDP01034 Mbuti_Pygmy_HGDP00450 5.7598<br />Biaka_Pygmy_HGDP00458 Biaka_Pygmy_HGDP00464Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-62739177112872255562016-07-09T07:50:41.649-07:002016-07-09T07:50:41.649-07:00Hi David, interesting post. I wonder wether it is...Hi David, interesting post. I wonder wether it is possible to share your code to create PCs based on IBD sharing inferred with BEAGLE fastIBD.<br /><br />Thanks!Anonymoushttps://www.blogger.com/profile/16151461890151467647noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-58250999187532598112014-08-14T13:48:34.166-07:002014-08-14T13:48:34.166-07:00Now that the new spreadsheets are out would someon...Now that the new spreadsheets are out would someone be able to please run my results for me? My Eurogenes id is CA1. I would appreciate it greatly if someone could. You can send my results to my email listed here. :)jackson_montgomery_devonihttps://www.blogger.com/profile/17553257488930856466noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-89170918647838690042014-08-12T18:58:40.079-07:002014-08-12T18:58:40.079-07:00Gui,
You might find this pairwise cM matrix inter...Gui,<br /><br />You might find this pairwise cM matrix interesting. It's in Past3 format, but can be opened with any spreadsheet software.<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQTXUwU0F2OFUzS2c/edit?usp=sharing<br /><br />It actually features West Eurasian and South Central Asian samples, so it might be useful for looking at gene flow between Western Europe and South Central Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-85677191141172425402014-08-12T18:53:10.782-07:002014-08-12T18:53:10.782-07:00Here are those datasheets. They should produce plo...Here are those datasheets. They should produce plots very similar to those above (West Eurasian, European and Finnish). I tried to include as many regular and not so regular contacts as possible. Apologies if I missed anyone out.<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQa1ZacUxwTFZpYm8/edit?usp=sharing<br /><br />You can run them with gnuplot. To get a 2D plot based on the first Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-9104808456736106042014-08-09T20:12:21.792-07:002014-08-09T20:12:21.792-07:00Would someone be able to run my results from the s...Would someone be able to run my results from the spreadsheets once David releases them please? My Eurogenes id is CA1. I do not know how to do this on my computer. You can send my results to this email. jackson_montgomery_devoni@hotmail.com<br /><br />If someone could do this I would greatly appreciate it.jackson_montgomery_devonihttps://www.blogger.com/profile/17553257488930856466noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-45447710884303797982014-08-09T09:11:46.142-07:002014-08-09T09:11:46.142-07:00Thank you David.Thank you David.jackson_montgomery_devonihttps://www.blogger.com/profile/17553257488930856466noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-80718122714268672922014-08-08T20:29:53.751-07:002014-08-08T20:29:53.751-07:00Hah, I was curious whether I was one of the green ...Hah, I was curious whether I was one of the green dots away from the French core on the plot with Jewish populations.<br /><br />Otherwise, I find it quite impressive how much the PCAs end up looking like IBS PCAs, what's the minimum segment length recognised as IBD for these.<br />Also, I wouldn't mind having a look at the distance matrixes, I feel like they could be interesting too.Gui Shttps://www.blogger.com/profile/10460980441040040539noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-81090265231211632872014-08-08T19:48:38.176-07:002014-08-08T19:48:38.176-07:00You'll be on the datasheets that I'll post...You'll be on the datasheets that I'll post later today. You'll have to run these with something like Past3 or Gnuplot.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-31293735643283879392014-08-08T19:42:34.665-07:002014-08-08T19:42:34.665-07:00David,
Am I or will I be on any of these plots?David,<br /><br />Am I or will I be on any of these plots?jackson_montgomery_devonihttps://www.blogger.com/profile/17553257488930856466noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-64797408003722952742014-08-08T19:39:02.495-07:002014-08-08T19:39:02.495-07:00Tesmos,
All of these plots are accurate, but each...Tesmos,<br /><br />All of these plots are accurate, but each one shows different things. So when you look at each plot have a think about what the components represent based on the samples that are featured. For instance, on the first plot dimension one is probably focusing on Near Eastern versus Northeast European ancestry. On the other hand, dimension one on the second plot seems to reflect Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-32333819629172034482014-08-08T03:47:59.006-07:002014-08-08T03:47:59.006-07:00@ David
Is it the same method that you used to di...@ David<br /><br />Is it the same method that you used to differentiate IBD from IBS at Eurogenes detective ?<br />I don't know if Iam in these PCAs, but if that's the case I ( FR20) am probably located with the British and not the French, being shifted East.Helgenes50https://www.blogger.com/profile/10048641344885582425noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-74711288847141975452014-08-08T03:41:42.955-07:002014-08-08T03:41:42.955-07:00Random ten samples from a country with 80 million ...Random ten samples from a country with 80 million people show less shared IBD-segments than from a populatio with 1.5 million people. I am not saying that the population structure has no effect on the results, but that the fundaments of usually seen PCAs are not adequate.Maurihttps://www.blogger.com/profile/03670078523265515878noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-61600101252792881802014-08-08T03:23:28.000-07:002014-08-08T03:23:28.000-07:00I think some of my family might be in this run: SE...I think some of my family might be in this run: SE36, FI16 and FSE1?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-39461771422797982192014-08-08T02:02:14.985-07:002014-08-08T02:02:14.985-07:00Davidsk which PCA plot should be most precise/accu...Davidsk which PCA plot should be most precise/accurate of the first four?Tesmoshttps://www.blogger.com/profile/02337218455886717264noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-9193571388123782882014-08-08T00:58:35.984-07:002014-08-08T00:58:35.984-07:00It's unlikely that you're on those PCA, bu...It's unlikely that you're on those PCA, but what's your ID?Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-7799631789097428552014-08-07T17:34:16.091-07:002014-08-07T17:34:16.091-07:00Nice work. Could you post some PCA with individual...Nice work. Could you post some PCA with individual Eurogenes IDs? Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-85370391032078642472014-08-07T16:18:26.024-07:002014-08-07T16:18:26.024-07:00Is there anything like a pc4? Using La Brana, Malt...Is there anything like a pc4? Using La Brana, Malta, mbuti, and Dai, maybe.Anonymoushttps://www.blogger.com/profile/13876988480444711159noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-71753681198494865512014-08-07T08:28:47.285-07:002014-08-07T08:28:47.285-07:00Groups showing low levels of cM sharing always get...Groups showing low levels of cM sharing always get squished by those showing excessive levels of cM sharing.<br /><br />It happened to the Near Eastern samples on the West Eurasian PCA. So in order to flesh out detail within the Near East, I'd have to remove the Northeastern Europeans and Scandinavians, and probably a few other groups as well.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-32126956706796129442014-08-07T08:22:34.138-07:002014-08-07T08:22:34.138-07:00Everybody got squished on the PCA with eastern fin...Everybody got squished on the PCA with eastern finns. How come?spagetiMeatballhttps://www.blogger.com/profile/01324633097628826684noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-5768748458734422602014-08-07T07:14:53.271-07:002014-08-07T07:14:53.271-07:00On the first PCA, I noticed that Greece spreads be...On the first PCA, I noticed that Greece spreads between Italy and the East Balkans.<br /><br />West Balkans is more extreme towards Belarus/Russia/Ukraine and Poland. It looks like the Slavic languages came down like a wedge into West Balkans.<br /><br />Interesting hints about migration path. Again hinted by deep R1a haplotype diversity in Kashubs and Sorbs. Are they preserving the Proto-Slav About Timehttps://www.blogger.com/profile/09236048173229545609noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-3658090032092862212014-08-07T06:21:34.820-07:002014-08-07T06:21:34.820-07:00David, you may be interested http://verenich.wordp...David, you may be interested http://verenich.wordpress.com/2014/07/26/%D0%B2%D0%B8%D0%B7%D1%83%D0%B0%D0%BB%D0%B8%D0%B7%D0%B0%D1%86%D0%B8%D1%8F-%D0%BA%D0%BE%D0%BB%D0%B8%D1%87%D0%B5%D1%81%D1%82%D0%B2%D0%B0-%D0%BE%D0%B1%D1%89%D0%B8%D1%85-ibd-%D1%81%D0%B5%D0%B3%D0%BC/Srkzhttps://www.blogger.com/profile/08713038610245740489noreply@blogger.com