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Greek and Slavic ancestry qpAdm models

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Dec 10th, 2023
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  1. ```c
  2. right = c('Mbuti.HO', 'Russia_Samara_EBA_Yamnaya', 'Russia_Karelia_HG', 'Serbia_IronGates_Mesolithic', 'Turkey_N', 'Iran_GanjDareh_N', 'Spain_IA', 'Greece_Minoan_Lassithi', 'Croatia_MLBA', 'Netherlands_EIA', 'Netherlands_MBA', 'Russia_IA_Ingria.SG', 'Latvia_BA', 'Turkey_EBA_II.SG', 'Israel_C', 'Armenia_EBA_KuraAraxes', 'Mongolia_North_N', 'Bulgaria_EIA', 'Croatia_EIA', 'Greece_BA_Mycenaean', 'Macedonia_Classical_Hellenistic', 'Russia_MLBA_Sintashta', 'Iran_C_SehGabi', 'Lebanon_MBA.SG')
  3.  
  4. left = c('Aegean(Roman_era_1-200AD).SG', 'Greece_Delphi_BA_Mycenaean', 'Russia_Sunghir_Medieval.SG')
  5.  
  6. target = c('Greek.HO')
  7.  
  8. results = qpadm(prefix, left, right, target, allsnps = TRUE)
  9. results$weights
  10. results$popdrop
  11. ```
  12. ```c
  13. P 0.0809
  14. target left weight se z
  15. <chr> <chr> <dbl> <dbl> <dbl>
  16. 1 Greek.HO Aegean(Roman_era_1-200AD).SG 0.621 0.0378 16.4
  17. 2 Greek.HO Albania_BA_IA 0.0278 0.0592 0.470
  18. 3 Greek.HO Russia_Sunghir_Medieval.SG 0.352 0.0295 11.9
  19. ```
  20. ```c
  21. P 0.114
  22. target left weight se z
  23. <chr> <chr> <dbl> <dbl> <dbl>
  24. 1 Greek.HO Aegean(Roman_era_1-200AD).SG 0.586 0.0597 9.81
  25. 2 Greek.HO Greece_Delphi_BA_Mycenaean 0.0560 0.0624 0.897
  26. 3 Greek.HO Russia_Sunghir_Medieval.SG 0.358 0.0166 21.5
  27. ```
  28. ```c
  29. right = c('Mbuti.HO', 'Russia_Samara_EBA_Yamnaya', 'Russia_Karelia_HG', 'Serbia_IronGates_Mesolithic', 'Turkey_N', 'Iran_GanjDareh_N', 'Spain_IA', 'Greece_Minoan_Lassithi', 'Croatia_MLBA', 'Netherlands_EIA', 'Netherlands_MBA', 'Russia_IA_Ingria.SG', 'Latvia_BA', 'Turkey_EBA_II.SG', 'Israel_C', 'Armenia_EBA_KuraAraxes', 'Mongolia_North_N', 'Bulgaria_EIA', 'Greece_BA_Mycenaean', 'Macedonia_Classical_Hellenistic', 'Russia_MLBA_Sintashta', 'Iran_C_SehGabi', 'Lebanon_MBA.SG')
  30.  
  31. left = c('Aegean(Roman_era_1-200AD).SG', 'Croatia_EIA', 'Russia_Sunghir_Medieval.SG')
  32.  
  33. target = c('Montenegro_Doclea_Roman.SG')
  34.  
  35. results = qpadm(prefix, left, right, target, allsnps = TRUE)
  36. results$weights
  37. results$popdrop
  38. ```
  39. ```c
  40. P 0.179
  41. target left weight se z
  42. <chr> <chr> <dbl> <dbl> <dbl>
  43. 1 Montenegro_Doclea_Roman.SG Aegean(Roman_era_1-200AD).SG 0.198 0.0423 4.67
  44. 2 Montenegro_Doclea_Roman.SG Croatia_EIA 0.126 0.0683 1.84
  45. 3 Montenegro_Doclea_Roman.SG Russia_Sunghir_Medieval.SG 0.676 0.0491 13.8
  46. ```
  47. ```c
  48. P 0.0457
  49. target left weight se z
  50. <chr> <chr> <dbl> <dbl> <dbl>
  51. 1 Croatian.HO Aegean(Roman_era_1-200AD).SG 0.249 0.0383 6.51
  52. 2 Croatian.HO Croatia_EIA 0.0529 0.0614 0.862
  53. 3 Croatian.HO Russia_Sunghir_Medieval.SG 0.698 0.0437 16.0
  54. ```
  55. ```c
  56. right = c('Mbuti.HO', 'Russia_Samara_EBA_Yamnaya', 'Russia_Karelia_HG', 'Serbia_IronGates_Mesolithic', 'Turkey_N', 'Iran_GanjDareh_N', 'Spain_IA', 'Greece_Minoan_Lassithi', 'Croatia_MLBA', 'Netherlands_EIA', 'Netherlands_MBA', 'Russia_IA_Ingria.SG', 'Latvia_BA', 'Turkey_EBA_II.SG', 'Israel_C', 'Armenia_EBA_KuraAraxes', 'Mongolia_North_N', 'Bulgaria_EIA', 'Greece_BA_Mycenaean', 'Macedonia_Classical_Hellenistic', 'Russia_MLBA_Sintashta', 'Iran_C_SehGabi', 'Croatia_EIA', 'Russia_Sunghir_Medieval.SG', 'Lebanon_MBA.SG')
  57.  
  58. left = c('Aegean(Roman_era_1-200AD).SG', 'Greece_Delphi_BA_Mycenaean', 'Montenegro_Doclea_Roman.SG')
  59.  
  60. target = c('Greek.HO')
  61.  
  62. results = qpadm(prefix, left, right, target, allsnps = TRUE)
  63. results$weights
  64. results$popdrop
  65. ```
  66. ```c
  67. P 0.278
  68. target left weight se z
  69. <chr> <chr> <dbl> <dbl> <dbl>
  70. 1 Greek.HO Aegean(Roman_era_1-200AD).SG 0.521 0.0408 12.8
  71. 2 Greek.HO Greece_Delphi_BA_Mycenaean -0.00820 0.0420 -0.195
  72. 3 Greek.HO Montenegro_Doclea_Roman.SG 0.487 0.0189 25.8
  73. ```
  74. ```c
  75. P 0.352
  76. target left weight se z
  77. <chr> <chr> <dbl> <dbl> <dbl>
  78. 1 Greek.HO Aegean(Roman_era_1-200AD).SG 0.514 0.0180 28.6
  79. 2 Greek.HO Montenegro_Doclea_Roman.SG 0.486 0.0180 27.0
  80. ```
  81. ```c
  82. right = c('Mbuti.HO', 'Russia_Samara_EBA_Yamnaya', 'Russia_Karelia_HG', 'Serbia_IronGates_Mesolithic', 'Turkey_N', 'Iran_GanjDareh_N', 'Spain_IA', 'Greece_Minoan_Lassithi', 'Croatia_MLBA', 'Netherlands_EIA', 'Netherlands_MBA', 'Russia_IA_Ingria.SG', 'Latvia_BA', 'Turkey_EBA_II.SG', 'Israel_C', 'Armenia_EBA_KuraAraxes', 'Mongolia_North_N', 'Bulgaria_EIA', 'Greece_BA_Mycenaean', 'Macedonia_Classical_Hellenistic', 'Russia_MLBA_Sintashta', 'Iran_C_SehGabi', 'Croatia_EIA')
  83.  
  84. left = c('Aegean(Roman_era_1-200AD).SG', 'Lebanon_MBA.SG', 'Russia_Sunghir_Medieval.SG', 'Tajikistan_Ksirov_Kushan')
  85.  
  86. target = c('Cypriot.HO')
  87.  
  88. results = qpadm(prefix, left, right, target, allsnps = TRUE)
  89. results$weights
  90. results$popdrop
  91. ```
  92. ```c
  93. P 0.0314
  94. target left weight se z
  95. <chr> <chr> <dbl> <dbl> <dbl>
  96. 1 Cypriot.HO Aegean(Roman_era_1-200AD).SG 0.643 0.0606 10.6
  97. 2 Cypriot.HO Lebanon_MBA.SG 0.246 0.0541 4.54
  98. 3 Cypriot.HO Russia_Sunghir_Medieval.SG 0.0353 0.0230 1.53
  99. 4 Cypriot.HO Tajikistan_Ksirov_Kushan 0.0763 0.0275 2.77
  100. ```
  101. ```c
  102. right = c('Mbuti.HO', 'Russia_Samara_EBA_Yamnaya', 'Russia_Karelia_HG', 'Serbia_IronGates_Mesolithic', 'Turkey_N', 'Iran_GanjDareh_N', 'Spain_IA', 'Greece_Minoan_Lassithi', 'Croatia_MLBA', 'Netherlands_EIA', 'Netherlands_MBA', 'Russia_IA_Ingria.SG', 'Latvia_BA', 'Turkey_EBA_II.SG', 'Israel_C', 'Armenia_EBA_KuraAraxes', 'Mongolia_North_N', 'Bulgaria_EIA', 'Greece_BA_Mycenaean', 'Macedonia_Classical_Hellenistic', 'Russia_MLBA_Sintashta', 'Iran_C_SehGabi', 'Croatia_EIA', 'Turkey_Alalakh_MLBA')
  103.  
  104. left = c('Aegean(Roman_era_1-200AD).SG', 'Lebanon_MBA.SG', 'Russia_Sunghir_Medieval.SG', 'Tajikistan_Ksirov_Kushan')
  105.  
  106. target = c('Cypriot.HO')
  107.  
  108. results = qpadm(prefix, left, right, target, allsnps = TRUE)
  109. results$weights
  110. results$popdrop
  111. ```
  112. ```c
  113. P 0.0217
  114. target left weight se z
  115. <chr> <chr> <dbl> <dbl> <dbl>
  116. 1 Cypriot.HO Aegean(Roman_era_1-200AD).SG 0.652 0.0603 10.8
  117. 2 Cypriot.HO Lebanon_MBA.SG 0.232 0.0530 4.38
  118. 3 Cypriot.HO Russia_Sunghir_Medieval.SG 0.0344 0.0235 1.47
  119. 4 Cypriot.HO Tajikistan_Ksirov_Kushan 0.0814 0.0273 2.98
  120. ```
  121. ```c
  122. right = c('Mbuti.HO', 'Russia_Samara_EBA_Yamnaya', 'Russia_Karelia_HG', 'Serbia_IronGates_Mesolithic', 'Turkey_N', 'Iran_GanjDareh_N', 'Spain_IA', 'Greece_Minoan_Lassithi', 'Croatia_MLBA', 'Netherlands_EIA', 'Netherlands_MBA', 'Russia_IA_Ingria.SG', 'Latvia_BA', 'Turkey_EBA_II.SG', 'Israel_C', 'Armenia_EBA_KuraAraxes', 'Mongolia_North_N', 'Bulgaria_EIA', 'Greece_BA_Mycenaean', 'Macedonia_Classical_Hellenistic', 'Russia_MLBA_Sintashta', 'Iran_C_SehGabi', 'Croatia_EIA', 'Turkey_Alalakh_MLBA', 'Tajikistan_Ksirov_Kushan')
  123.  
  124. left = c('Aegean(Roman_era_1-200AD).SG', 'Lebanon_MBA.SG', 'Russia_Sunghir_Medieval.SG')
  125.  
  126. target = c('Cypriot.HO')
  127. ```
  128. ```c
  129. P 0.000377
  130. target left weight se z
  131. <chr> <chr> <dbl> <dbl> <dbl>
  132. 1 Cypriot.HO Aegean(Roman_era_1-200AD).SG 0.639 0.0641 9.97
  133. 2 Cypriot.HO Lebanon_MBA.SG 0.283 0.0527 5.36
  134. 3 Cypriot.HO Russia_Sunghir_Medieval.SG 0.0780 0.0176 4.43
  135. ```
  136. ```c
  137. right = c('Mbuti.HO', 'Russia_Samara_EBA_Yamnaya', 'Russia_Karelia_HG', 'Serbia_IronGates_Mesolithic', 'Turkey_N', 'Iran_GanjDareh_N', 'Spain_IA', 'Greece_Minoan_Lassithi', 'Croatia_MLBA', 'Netherlands_EIA', 'Netherlands_MBA', 'Russia_IA_Ingria.SG', 'Latvia_BA', 'Turkey_EBA_II.SG', 'Israel_C', 'Armenia_EBA_KuraAraxes', 'Mongolia_North_N', 'Croatia_EIA', 'Greece_BA_Mycenaean', 'Macedonia_Classical_Hellenistic', 'Russia_MLBA_Sintashta', 'Iran_C_SehGabi', 'Lebanon_MBA.SG')
  138.  
  139. left = c('Aegean(Roman_era_1-200AD).SG', 'Bulgaria_EIA', 'Russia_Sunghir_Medieval.SG')
  140.  
  141. target = c('Bulgarian.HO')
  142.  
  143. results = qpadm(prefix, left, right, target, allsnps = TRUE)
  144. results$weights
  145. results$popdrop
  146. ```
  147. ```c
  148. P 0.0271
  149. target left weight se z
  150. <chr> <chr> <dbl> <dbl> <dbl>
  151. 1 Bulgarian.HO Aegean(Roman_era_1-200AD).SG 0.452 0.0512 8.81
  152. 2 Bulgarian.HO Bulgaria_EIA 0.000506 0.0551 0.00918
  153. 3 Bulgarian.HO Russia_Sunghir_Medieval.SG 0.548 0.0248 22.1
  154.  
  155. P 0.4.93e- 14
  156. target left weight se z
  157. <chr> <chr> <dbl> <dbl> <dbl>
  158. 1 Bulgarian.HO Bulgaria_EIA 0.374 0.0308 12.2
  159. 2 Bulgarian.HO Russia_Sunghir_Medieval.SG 0.626 0.0308 20.3
  160. ```
  161. ```c
  162. right = c('Mbuti.HO', 'Russia_Samara_EBA_Yamnaya', 'Russia_Karelia_HG', 'Serbia_IronGates_Mesolithic', 'Turkey_N', 'Iran_GanjDareh_N', 'Spain_IA', 'Greece_Minoan_Lassithi', 'Croatia_MLBA', 'Netherlands_EIA', 'Netherlands_MBA', 'Russia_IA_Ingria.SG', 'Latvia_BA', 'Turkey_EBA_II.SG', 'Israel_C', 'Armenia_EBA_KuraAraxes', 'Mongolia_North_N', 'Croatia_EIA', 'Greece_BA_Mycenaean', 'Macedonia_Classical_Hellenistic', 'Russia_MLBA_Sintashta', 'Iran_C_SehGabi', 'Lebanon_MBA.SG', 'Bulgaria_EIA')
  163.  
  164. left = c('Aegean(Roman_era_1-200AD).SG', 'Albania_BA_IA', 'Russia_Sunghir_Medieval.SG')
  165.  
  166. target = c('Bulgarian.HO')
  167.  
  168. results = qpadm(prefix, left, right, target, allsnps = TRUE)
  169. results$weights
  170. results$popdrop
  171. ```
  172. ```c
  173. P 0.0389
  174. target left weight se z
  175. <chr> <chr> <dbl> <dbl> <dbl>
  176. 1 Bulgarian.HO Aegean(Roman_era_1-200AD).SG 0.430 0.0512 8.41
  177. 2 Bulgarian.HO Albania_BA_IA 0.0394 0.0796 0.495
  178. 3 Bulgarian.HO Russia_Sunghir_Medieval.SG 0.530 0.0403 13.2
  179. ```
  180. ```c
  181. P 0.203
  182. target left weight se z
  183. <chr> <chr> <dbl> <dbl> <dbl>
  184. 1 Croatian.HO Aegean(Roman_era_1-200AD).SG 0.0174 0.0290 0.601
  185. 2 Croatian.HO Montenegro_Doclea_Roman.SG 0.983 0.0290 33.9
  186. ```
  187. ```c
  188. P 0.0293
  189. target left weight se z
  190. <chr> <chr> <dbl> <dbl> <dbl>
  191. 1 Albanian.HO Aegean(Roman_era_1-200AD).SG 0.505 0.0452 11.2
  192. 2 Albanian.HO Albania_BA_IA 0.124 0.0700 1.77
  193. 3 Albanian.HO Russia_Sunghir_Medieval.SG 0.371 0.0365 10.2
  194. ```
  195. ```c
  196. P 0.0153
  197. target left weight se z
  198. <chr> <chr> <dbl> <dbl> <dbl>
  199. 1 Albanian.HO Aegean(Roman_era_1-200AD).SG 0.500 0.0485 10.3
  200. 2 Albanian.HO Bulgaria_EIA 0.0913 0.0522 1.75
  201. 3 Albanian.HO Russia_Sunghir_Medieval.SG 0.409 0.0240 17.1
  202. ```
  203. ```c
  204. right = c('Mbuti.HO', 'Russia_Samara_EBA_Yamnaya', 'Russia_Karelia_HG', 'Serbia_IronGates_Mesolithic', 'Turkey_N', 'Iran_GanjDareh_N', 'Spain_IA', 'Greece_Minoan_Lassithi', 'Croatia_MLBA', 'Netherlands_EIA', 'Netherlands_MBA', 'Russia_IA_Ingria.SG', 'Latvia_BA', 'Turkey_EBA_II.SG', 'Israel_C', 'Armenia_EBA_KuraAraxes', 'Mongolia_North_N', 'Bulgaria_EIA', 'Greece_BA_Mycenaean', 'Macedonia_Classical_Hellenistic', 'Russia_MLBA_Sintashta', 'Iran_C_SehGabi', 'Lebanon_MBA.SG', 'Croatia_EIA', 'Russia_Sunghir_Medieval.SG', 'Aegean(Roman_era_1-200AD).SG')
  205.  
  206. left = c('Montenegro_Doclea_Roman.SG')
  207.  
  208. target = c('Croatian.HO')
  209.  
  210. results = qpadm(prefix, left, right, target, allsnps = TRUE)
  211. results$weights
  212. results$popdrop
  213. ```
  214. ```c
  215. P 0.249
  216. target left weight se z
  217. <chr> <chr> <dbl> <dbl> <dbl>
  218. 1 Croatian.HO Montenegro_Doclea_Roman.SG 1 1.14e-13 8.79e12
  219. ```
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