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, k=23, mixedmode=T)
Originally Posted by Jackson
Cheers.
And mixedmode is TOracle(c(X), mixedmode=T, k=23) i think?
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Ok here's my oracle and mixedmode, it's in the right ballpark for sure, although some of the populations look a bit muddled and i'm too close to Scandinavians going by experience. Although that said i am pretty close to my actual population, and other close ones are not a great distance away for the most part (<5 or <10).
[1,] "English" "2.3543"
[2,] "N._European" "2.9094"
[3,] "Belgian" "4.077"
[4,] "Norwegian" "4.1493"
[5,] "Dutch" "4.2092"
[6,] "Icelandic" "4.2266"
[7,] "Mixed_German" "4.3609"
[8,] "CEU" "4.7685"
[9,] "Swede" "4.8957"
[10,] "English_Kent_GBR" "5.4688"
[11,] "North_German" "5.515"
[12,] "English_Cornwall_GBR" "5.5796"
[13,] "South-German" "5.5908"
[14,] "Welsh" "5.663"
[15,] "Scottish_Argyll_Bute_GBR" "5.728"
[16,] "Mixed_European" "5.7284"
[17,] "Orcadian" "6.613"
[18,] "Swedish" "7.0239"
[19,] "United-Kingdom" "8.0472"
[20,] "Germans" "8.5695"
[21,] "Austrian" "9.8511"
[22,] "French" "9.9629"
[23,] "British" "10.1624"
[1,] "82% Icelandic + 18% Maltese" "0.4331"
[2,] "16% French_Jew + 84% Icelandic" "0.6635"
[3,] "84.7% Icelandic + 15.3% Moroccan_Jew" "0.6701"
[4,] "15.1% Moroccan_Jew + 84.9% Norwegian" "0.6754"
[5,] "85% Icelandic + 15% Italian_Jew" "0.6759"
[6,] "87% Norwegian + 13% Tunisian_Jew" "0.7342"
[7,] "84.8% Icelandic + 15.2% Sephardic_Jews" "0.8372"
[8,] "13.9% Libyan_Jew + 86.1% Norwegian" "0.8375"
[9,] "85.2% Icelandic + 14.8% Turkish_Jew" "0.8405"
[10,] "86.8% Icelandic + 13.2% Tunisian_Jew" "0.8422"
[11,] "85.9% Icelandic + 14.1% Libyan_Jew" "0.9024"
[12,] "85.1% Norwegian + 14.9% Sephardic_Jews" "0.9345"
[13,] "17.5% Maltese + 82.5% Norwegian" "0.9404"
[14,] "14.6% Italian_Jew + 85.4% Norwegian" "0.9617"
[15,] "15.5% French_Jew + 84.5% Norwegian" "0.9837"
[16,] "85.5% Norwegian + 14.5% Turkish_Jew" "0.9868"
[17,] "83.8% Icelandic + 16.2% Sicilian" "1.0405"
[18,] "16.8% Ashkenazi_Jew + 83.2% Icelandic" "1.0541"
[19,] "83.5% Icelandic + 16.5% Italian_EastSicilian" "1.0712"
[20,] "96% English + 4% Moroccans" "1.1232"
[21,] "81.2% Icelandic + 18.8% Italian_WestSicilian" "1.2093"
[22,] "95.3% English + 4.7% Tunisian" "1.2121"
[23,] "16.3% Ashkenazi_Jew + 83.7% Norwegian" "1.2737"
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Where is the rest ?
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My Grandfather:
0.09% Amerindian
4.13% Ancestral-North-Eura
6.70% Ancestral-North-Indi
0.06% Arctic
0.33% Ancestral-South-Indi
0.03% Austroloid
0.02% Austronesian
19.28% Caucasian
0.00% Archaic-Human
0.10% East-African
0.07% East-Siberian
27.93% European_Early_Farme
0.03% Khoisan
0.03% Melano-Polinesian
0.00% Archaic-African
0.66% Near-East
1.82% North-African
0.13% Paleo-Siberian
0.08% African-Pygmy
0.03% South-East-Asian
0.01% Subsaharian
0.01% AltaiŃ
38.46% European_Hunters_Gat
[1,] "N._European" "1.5645"
[2,] "English" "1.5871"
[3,] "CEU" "3.2323"
[4,] "Norwegian" "3.2973"
[5,] "Icelandic" "3.4797"
[6,] "Belgian" "3.7227"
[7,] "Mixed_German" "4.0018"
[8,] "English_Cornwall_GBR" "4.1035"
[9,] "Welsh" "4.1038"
[10,] "English_Kent_GBR" "4.189"
[11,] "Scottish_Argyll_Bute_GBR" "4.237"
[12,] "Dutch" "4.568"
[13,] "Orcadian" "5.2656"
[14,] "Swede" "5.5832"
[15,] "South-German" "6.1043"
[16,] "North_German" "6.2343"
[17,] "Mixed_European" "6.5827"
[18,] "United-Kingdom" "7.469"
[19,] "Swedish" "7.8954"
[20,] "British" "8.8517"
[1,] "3.2% Afghan_Pushtun + 96.8% N._European" "0.8007"
[2,] "2.3% Makrani + 97.7% N._European" "0.8105"
[3,] "2.2% Balochi + 97.8% N._European" "0.8141"
[4,] "97.1% N._European + 2.9% Pashtun" "0.8224"
[5,] "2% Brahui + 98% N._European" "0.8316"
[6,] "96.8% N._European + 3.2% Tajik_Pomiri" "0.834"
[7,] "1.9% Kalash + 98.1% N._European" "0.8563"
[8,] "96.6% N._European + 3.4% Tadjik" "0.8891"
[9,] "97.6% N._European + 2.4% Pathan" "0.9561"
[10,] "97.2% N._European + 2.8% Parsi" "0.9687"
[11,] "3.1% Iranian + 96.9% N._European" "0.9842"
[12,] "31.5% Bosnian + 68.5% British" "0.9959"
[13,] "97.9% N._European + 2.1% Sindhi" "1.0087"
[14,] "97.5% N._European + 2.5% Pakistani_Pushtun" "1.0221"
[15,] "97.9% N._European + 2.1% Punjabi-Gujjar" "1.0255"
[16,] "2.3% Burusho + 97.7% N._European" "1.0317"
[17,] "97.2% N._European + 2.8% Tabassaran" "1.0451"
[18,] "2.7% Lak + 97.3% N._European" "1.0571"
[19,] "2.9% Kurd + 97.1% N._European" "1.0651"
[20,] "2.7% Lezgins + 97.3% N._European" "1.0661"
Last edited by Jackson; 09-11-2014 at 09:47 PM.
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I don't know how to run Oracle. Your command doesn't work for me, for some reason.
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Frisian:
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------
0.07% Amerindian
6.92% Ancestral-North-Eura
7.87% Ancestral-North-Indi
0.05% Arctic
0.31% Ancestral-South-Indi
0.01% Austroloid
0.03% Austronesian
19.99% Caucasian
0.00% Archaic-Human
0.01% East-African
0.11% East-Siberian
24.89% European_Early_Farme
0.00% Khoisan
0.06% Melano-Polinesian
0.00% Archaic-African
0.84% Near-East
0.53% North-African
0.03% Paleo-Siberian
0.00% African-Pygmy
0.04% South-East-Asian
0.01% Subsaharian
0.05% AltaiŃ
38.17% European_Hunters_Gat
[1,] "Dutch" "3.1598"
[2,] "English" "4.4481"
[3,] "Swede" "4.6727"
[4,] "Icelandic" "4.7767"
[5,] "Norwegian" "4.8579"
[6,] "N._European" "5.3847"
[7,] "Belgian" "5.5866"
[8,] "North_German" "5.9357"
[9,] "Swedish" "6.029"
[10,] "Mixed_European" "6.0491"
[11,] "Scottish_Argyll_Bute_GBR" "6.4995"
[12,] "CEU" "6.5913"
[13,] "English_Cornwall_GBR" "6.9943"
[14,] "Mixed_German" "7.2488"
[15,] "South-German" "7.2841"
[16,] "English_Kent_GBR" "7.388"
[17,] "Welsh" "7.5862"
[18,] "Orcadian" "7.62"
[19,] "United-Kingdom" "9.9122"
[20,] "Germans" "10.007"
[21,] "Austrian" "10.261"
[22,] "Mixed_CEU" "10.6238"
[23,] "British" "11.2503"
[1,] "86.8% Norwegian + 13.2% Stalskoe" "1.0279"
[2,] "10.8% Chechen + 89.2% Norwegian" "1.0358"
[3,] "88.9% Norwegian + 11.1% Urkarah" "1.0372"
[4,] "11.1% Lezgin + 88.9% Norwegian" "1.0687"
[5,] "11.2% Lak + 88.8% Norwegian" "1.1208"
[6,] "10.9% Avar + 89.1% Norwegian" "1.1239"
[7,] "10.9% Lezgins + 89.1% Norwegian" "1.1389"
[8,] "11.3% Kumyk + 88.7% Norwegian" "1.2438"
[9,] "11.1% Azeri_Dagestan + 88.9% Norwegian" "1.2808"
[10,] "10.5% Chechen + 89.5% Icelandic" "1.3052"
[11,] "10.5% Adygei + 89.5% Norwegian" "1.3164"
[12,] "89% Norwegian + 11% Tabassaran" "1.3557"
[13,] "10.3% North_Ossetian + 89.7% Norwegian" "1.3735"
[14,] "87.2% Icelandic + 12.8% Stalskoe" "1.3888"
[15,] "10.3% Adygei + 89.7% Icelandic" "1.3941"
[16,] "89.9% Icelandic + 10.1% North_Ossetian" "1.4139"
[17,] "90.2% Norwegian + 9.8% Ossetian" "1.4215"
[18,] "10.3% Balkar + 89.7% Norwegian" "1.4333"
[19,] "8.5% Abkhasian + 91.5% Icelandic" "1.4547"
[20,] "10.2% Balkar + 89.8% Icelandic" "1.4566"
[21,] "89% Icelandic + 11% Kumyk" "1.4633"
[22,] "91.8% Icelandic + 8.2% Svan" "1.4706"
[23,] "90.4% Icelandic + 9.6% Ossetian" "1.504"
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Okay show me the steps I'll help you
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I have R 2.13.1 and DIYDodecad2.1, and all the runs work if i follow the Readme file.
But the command TOracle doesn't get recognized in R. I'm probably missing some Oracle files.
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37.40% European_Hunters_Gatherer
28.74% European_Early_Farmer
19.82% Caucasian
6.13% Ancestral-North-Indian
5.00% Ancestral-North-Eurasian
[1,] "English" "1.8047"
[2,] "N._European" "1.8145"
[3,] "CEU" "2.5489"
[4,] "Belgian" "2.7917"
[5,] "English_Kent_GBR" "2.9429"
[6,] "English_Cornwall_GBR" "3.0063"
[7,] "Mixed_German" "3.2741"
[8,] "Norwegian" "3.4227"
[9,] "Welsh" "3.5037"
[10,] "Icelandic" "3.9039"
Mixed Mode
[1,] "81.6% English_Cornwall_GBR + 18.4% Mixed_CEU" "0.7387"
[2,] "60.5% Belgian + 39.5% Scottish_Argyll_Bute_GBR" "0.7752"
[3,] "66.2% CEU + 33.8% Dutch" "0.7932"
Last edited by Graham; 09-12-2014 at 02:56 PM.
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After you got the admixture results first load workspace and select TOracle: copy and paste this command TOracle(c(X), k=23)
and place where the X is your results:
Example: TOracle(c(0.01, 5.33, 6.63, 0.04, 0.16, 0.06, 0.06, 20.23, 0.01, 0.09, 0.07, 24.99, 0.01, 0.03, 0.02, 0.64, 1.29, 0.02, 0.20, 0.02, 0.03, 0.04, 40.04), k=23)
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