@Kaspias
I am glad that my post helped. Nice to see that you too have managed to run it!
@Zoro
Very helpful advices all around. Thanks again.
---
So I made a few more runs (maxmiss=0 and 93k~ snps ) using the 1240K dataset and the following populations. I picked Tepecik for Neolithic Anatolia. Open for suggestions!
Code:
right= c('Russia_DevilsCave_N.SG','Switzerland_Bichon.SG','Morocco_Iberomaurusian','Turkey_TepecikCiftlik_N.SG','Georgia_Kotias.SG','Russia_HG_Karelia', 'Russia_Yana_UP.SG', 'Iran_GanjDareh_N', 'Russia_Kolyma_M.SG')
left = c("Bulgarian.DG","Adygei.DG","Turkmen.SG",'Georgian.DG','Greek_1.DG')
This seems to be the best result, standard errors can go lower I guess. The p values seem OK
About the z values corresponding to weight estimations: What is being tested here? weight i = 0 ? It seems like it.
Also, why do we want to fail to reject the model hypothesis? Can't seem to find a layman interpretation (no surprise).
Run 1: (Greek and Bulgarian did not go well together and Greek instead of Bulgarian yielded better results..Georgian seems to be a non-factor here: not significantly different than 0. But I would expect to have around 10%. Adygei on the other hand has a high se here, possibly due to its rather close proximity to Georgian.)
Code:
=======================================
target left weight se z
---------------------------------------
1 me Adygei.DG 0.436 0.267 1.636
2 me Turkmen.SG 0.051 0.049 1.055
3 me Georgian.DG 0.053 0.2 0.263
4 me Greek_1.DG 0.46 0.127 3.617
---------------------------------------
the p value = 0.56
====================================================
f4rank dof chisq p dofdiff chisqdiff p_nested
----------------------------------------------------
1 3 5 3.924 0.56 7 36.838 0
2 2 12 40.761 0 9 101.281 0
3 1 21 142.042 0 11 732.627 0
4 0 32 874.67 0 NA NA NA
----------------------------------------------------
Another run, without Georgian. (Adygei SE is now 0.15)
Code:
======================================
target left weight se z
--------------------------------------
1 me Adygei.DG 0.489 0.15 3.268
2 me Turkmen.SG 0.046 0.045 1.006
3 me Greek_1.DG 0.466 0.13 3.584
--------------------------------------
=====================================================
f4rank dof chisq p dofdiff chisqdiff p_nested
-----------------------------------------------------
1 2 6 3.965 0.681 8 68.9 0
2 1 14 72.865 0 10 653.942 0
3 0 24 726.807 0 NA NA NA
-----------------------------------------------------
bonus 1: me vs the populations I used (f2 statistics). If I am interpreting these correctly it says I am closer to Bulgarians than the Adygei (albeit not by a significant margin). On g25 I get the opposite all the time, with a clear margin.
Code:
====================================================================
pop1 pop2 est se z p
--------------------------------------------------------------------
1 me Bulgarian.DG 9e-04 0.0011 0.82034 0.41202
2 me Adygei.DG 0.00134 0.00116 1.14901 0.25055
3 me Georgian.DG 0.00232 0.00111 2.09104 0.03652
4 me Greek_1.DG 0.00301 0.00148 2.03656 0.04169
5 me Iran_GanjDareh_N 0.0566 0.00121 46.81045 0
6 me Turkmen.SG 0.06436 0.00126 51.18922 0
7 me Russia_Yana_UP.SG 0.08537 0.00142 60.25923 0
8 me Morocco_Iberomaurusian 0.09281 0.0014 66.0843 0
9 me Russia_DevilsCave_N.SG 0.10113 0.00151 66.87772 0
10 me Turkey_TepecikCiftlik_N.SG 0.13288 0.00139 95.47373 0
11 me Russia_HG_Karelia 0.16392 0.00155 106.00861 0
12 me Georgia_Kotias.SG 0.17455 0.00155 112.48209 0
13 me Switzerland_Bichon.SG 0.17911 0.00175 102.16275 0
14 me Russia_Kolyma_M.SG 0.19436 0.00177 109.87032 0
--------------------------------------------------------------------
]
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