prefix = "C:/Users/1l16m/Downloads/qpAdm_files/1240K+HO/v54.1.p1_HO_public"
library(admixtools)
library(tidyverse)
target = c('Greek_1.DG')
left= c('Spain_Greek_oAegean','Polish.DG','Armenian.DG')
right = c('Mbuti.DG', 'Ethiopia_4500BP.SG', 'Russia_Ust_Ishim.DG', 'Czech_Vestonice16', 'Belgium_UP_GoyetQ116_1', 'Russia_Kostenki14.SG', 'Russia_AfontovaGora3', 'Italy_North_Villabruna_HG', 'Han.DG', 'Papuan.DG', 'Karitiana.DG', 'Georgia_Satsurblia.SG', 'Iran_GanjDareh_N', 'Turkey_Epipaleolithic', 'Morocco_Iberomaurusian', 'Jordan_PPNB', 'Russia_Karelia_HG.SG', 'Russia_Samara_EBA_Yamnaya', 'Czech_CordedWare', 'Armenia_LBA.SG', 'ONG.SG')
mypops = c('Mbuti.DG', 'Ethiopia_4500BP.SG', 'Russia_Ust_Ishim.DG', 'Czech_Vestonice16', 'Belgium_UP_GoyetQ116_1', 'Russia_Kostenki14.SG', 'Russia_AfontovaGora3', 'Italy_North_Villabruna_HG', 'Han.DG', 'Papuan.DG', 'Karitiana.DG', 'Georgia_Satsurblia.SG', 'Iran_GanjDareh_N', 'Turkey_Epipaleolithic', 'Morocco_Iberomaurusian', 'Jordan_PPNB', 'Russia_Karelia_HG.SG', 'Russia_Samara_EBA_Yamnaya', 'Czech_CordedWare', 'Armenia_LBA.SG', 'ONG.SG','Greek_1.DG','Spain_Greek_oAegean','Polish.DG','Armenian.DG')
results = qpadm(prefix, left, right, target, allsnps = TRUE)
results$weights
results$popdrop
Greek_1.DG = 37.4% Spain_Greek_oAegean + 53.9% Polish.DG + 8.71% Armenian.DG
Looks a lot more Polish than your result, maybe I picked different Greek sample, near Bulgarian border?
I will add the other two Emporion samples -
I8208 and I8205 - which are both under label 'Spain_Hellenistic_oAegean' in the latest v54.1.p1_HO_public
target = c('Greek_1.DG')
left= c('Spain_Greek_oAegean',
'Spain_Hellenistic_oAegean','Polish.DG','Armenian.DG')
right = c('Mbuti.DG', 'Ethiopia_4500BP.SG', 'Russia_Ust_Ishim.DG', 'Czech_Vestonice16', 'Belgium_UP_GoyetQ116_1', 'Russia_Kostenki14.SG', 'Russia_AfontovaGora3', 'Italy_North_Villabruna_HG', 'Han.DG', 'Papuan.DG', 'Karitiana.DG', 'Georgia_Satsurblia.SG', 'Iran_GanjDareh_N', 'Turkey_Epipaleolithic', 'Morocco_Iberomaurusian', 'Jordan_PPNB', 'Russia_Karelia_HG.SG', 'Russia_Samara_EBA_Yamnaya', 'Czech_CordedWare', 'Armenia_LBA.SG', 'ONG.SG')
mypops = c('Mbuti.DG', 'Ethiopia_4500BP.SG', 'Russia_Ust_Ishim.DG', 'Czech_Vestonice16', 'Belgium_UP_GoyetQ116_1', 'Russia_Kostenki14.SG', 'Russia_AfontovaGora3', 'Italy_North_Villabruna_HG', 'Han.DG', 'Papuan.DG', 'Karitiana.DG', 'Georgia_Satsurblia.SG', 'Iran_GanjDareh_N', 'Turkey_Epipaleolithic', 'Morocco_Iberomaurusian', 'Jordan_PPNB', 'Russia_Karelia_HG.SG', 'Russia_Samara_EBA_Yamnaya', 'Czech_CordedWare', 'Armenia_LBA.SG', 'ONG.SG','Greek_1.DG','Spain_Greek_oAegean',
'Spain_Hellenistic_oAegean','Polish.DG','Armenian.DG')
results = qpadm(prefix, left, right, target, allsnps = TRUE)
results$weights
results$popdrop
Greek_1.DG = -27.7% Spain_Greek_oAegean + 65% Spain_Hellenistic_oAegean + 61.9% Polish.DG + 0.781% Armenian.DG
Is it possible to forbid modeling with negative values?