Academic qpAdm Model Replication

[Jovialis]

With a big thanks to Maciamo for creating it, we are proud to announce the creation of the Admixtools sub-forum!

This thread will be dedicated to the re-creation of qpadm models from academic papers.
The object of the thread is to post FAM or Ind files that are modified to replicate a select study of your choice. As well discovery of novel insights based on those replications.

Since I already did one myself, here is the FAM for a replication of Raveane et al. 2022:

v54.1.p1_HO_Raveane_2022

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[Jovialis]

Sarno et al. 2021

v54.1.p1_HO_Sarno_2021

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Prompt

# Define paths for dataset
prefix = "D:\\Bioinformatics\\01_Admixtools_Dataset\\v54.1.p1_HO_Jovialis_Plink\\v54.1.p1_HO_Jovialis"
my_f2_dir = "D:\\Bioinformatics\\my_f2_dir_Jovialis"


# Load necessary libraries
library(admixtools)
library(tidyverse)


# Define populations
target = c('Italian_South.HO')  # Update this if your sample has a different name in the merged dataset
left = c('Steppe_EMBA', 'Anatolia_N', 'WHG', 'CHG_Iran_N')


# Right list
right = c('Ust_Ishim', 'Kostenki14', 'MA1_HG', 'Goyet', 'ElMiron', 'Vestonice16', 'Villabruna', 'EHG', 'Levant_N', 'Natufian', 'Mota')


# Generate f2 stats
mypops = c(right, target, left)
extract_f2(prefix, my_f2_dir, pops = mypops, overwrite = TRUE, maxmiss = 1)
f2_blocks = f2_from_precomp(my_f2_dir, pops = mypops, afprod = TRUE)


# Run the model
results = qpadm(prefix, left, right, target, allsnps = TRUE)
results$weights
results$popdrop

Jovialis

Steppe_EMBA: 21.3%
Anatolia_N: 47.3%
WHG: 5.72%
CHG_Iran_N: 25.8%

Italian_South.HO

Steppe_EMBA: 17.9%
Anatolia_N: 56%
WHG: 1.58%
CHG_Iran_N: 24.5%

Italian_North.HO

Steppe: 28.3%
Anatolia_N: 56.6%
WHG: 6.89%
CHG_Iran_N: 14.2%

> results$weights
# A tibble: 4 × 5
target   left        weight     se     z
<chr>    <chr>        <dbl>  <dbl> <dbl>
1 Jovialis Steppe_EMBA 0.213  0.0729  2.92
2 Jovialis Anatolia_N  0.473  0.0534  8.85
3 Jovialis WHG         0.0572 0.0278  2.05
4 Jovialis CHG_Iran_N  0.258  0.0829  3.11
> results$popdrop
# A tibble: 15 × 15
pat      wt   dof   chisq         p f4rank Steppe_EMBA Anatolia_N     WHG CHG_Iran_N feasible best  dofdiff chisqdiff p_nested
<chr> <dbl> <dbl>   <dbl>     <dbl>  <dbl>       <dbl>      <dbl>   <dbl>      <dbl> <lgl>    <lgl>   <dbl>     <dbl>    <dbl>
1 0000      0     7    3.88 7.93e-  1      3      0.213       0.473  0.0572      0.258 TRUE     NA         NA      NA         NA
2 0001      1     8   42.1  1.30e-  6      2      0.377       0.605  0.0182     NA     TRUE     TRUE        0      26.2        0
3 0010      1     8   15.9  4.32e-  2      2      0.302       0.494 NA           0.204 TRUE     TRUE        0    -148.         1
4 0100      1     8  164.   2.60e- 31      2     -0.173      NA      0.189       0.984 FALSE    TRUE        0     122.         0
5 1000      1     8   41.6  1.59e-  6      2     NA           0.455  0.105       0.439 TRUE     TRUE       NA      NA         NA
6 0011      2     9   56.5  6.28e-  9      1      0.391       0.609 NA          NA     TRUE     NA         NA      NA         NA
7 0101      2     9  836.   3.01e-174      1      1.10       NA     -0.101      NA     FALSE    NA         NA      NA         NA
8 0110      2     9  282.   1.55e- 55      1      0.0390     NA     NA           0.961 TRUE     NA         NA      NA         NA
9 1001      2     9  340.   1.03e- 67      1     NA           0.886  0.114      NA     TRUE     NA         NA      NA         NA
10 1010      2     9  138.   2.28e- 25      1     NA           0.498 NA           0.502 TRUE     NA         NA      NA         NA
11 1100      2     9  248.   3.10e- 48      1     NA          NA      0.132       0.868 TRUE     NA         NA      NA         NA
12 0111      3    10  949.   1.56e-197      0      1          NA     NA          NA     TRUE     NA         NA      NA         NA
13 1011      3    10  444.   3.61e- 89      0     NA           1     NA          NA     TRUE     NA         NA      NA         NA
14 1101      3    10 1695.   0              0     NA          NA      1          NA     TRUE     NA         NA      NA         NA
15 1110      3    10  348.   1.17e- 68      0     NA          NA     NA           1     TRUE     NA         NA      NA         NA


> results$weights
# A tibble: 4 × 5
target           left        weight     se     z
<chr>            <chr>        <dbl>  <dbl> <dbl>
1 Italian_South.HO WHG         0.0158 0.0134  1.18
2 Italian_South.HO CHG_Iran_N  0.245  0.0431  5.68
3 Italian_South.HO Steppe_EMBA 0.179  0.0360  4.97
4 Italian_South.HO Anatolia_N  0.560  0.0267 21.0
> results$popdrop
# A tibble: 15 × 15
pat      wt   dof  chisq         p f4rank     WHG CHG_Iran_N Steppe_EMBA Anatolia_N feasible best  dofdiff chisqdiff p_nested
<chr> <dbl> <dbl>  <dbl>     <dbl>  <dbl>   <dbl>      <dbl>       <dbl>      <dbl> <lgl>    <lgl>   <dbl>     <dbl>    <dbl>
1 0000      0     7   11.5 1.18e-  1      3  0.0158      0.245       0.179      0.560 TRUE     NA         NA      NA         NA
2 0001      1     8  287.  2.45e- 57      2  0.172       1.18       -0.353     NA     FALSE    TRUE        0     233.         0
3 0010      1     8   53.6 8.39e-  9      2  0.0497      0.416      NA          0.534 TRUE     TRUE        0     -22.4        1
4 0100      1     8   76.0 3.10e- 13      2 -0.0146     NA           0.332      0.682 FALSE    TRUE        0      60.0        0
5 1000      1     8   16.0 4.18e-  2      2 NA           0.232       0.197      0.571 TRUE     TRUE       NA      NA         NA
6 0011      2     9  452.  1.03e- 91      1  0.0677      0.932      NA         NA     TRUE     NA         NA      NA         NA
7 0101      2     9 1378.  4.22e-291      1 -0.499      NA           1.50      NA     FALSE    NA         NA      NA         NA
8 0110      2     9  418.  2.28e- 84      1  0.0668     NA          NA          0.933 TRUE     NA         NA      NA         NA
9 1001      2     9  393.  4.06e- 79      1 NA           1.18       -0.176     NA     FALSE    NA         NA      NA         NA
10 1010      2     9   87.8 4.39e- 15      1 NA           0.446      NA          0.554 TRUE     NA         NA      NA         NA
11 1100      2     9   93.6 3.14e- 16      1 NA          NA           0.314      0.686 TRUE     NA         NA      NA         NA
12 0111      3    10 2241.  0              0  1          NA          NA         NA     TRUE     NA         NA      NA         NA
13 1011      3    10  491.  3.02e- 99      0 NA           1          NA         NA     TRUE     NA         NA      NA         NA
14 1101      3    10 1912.  0              0 NA          NA           1         NA     TRUE     NA         NA      NA         NA
15 1110      3    10  484.  1.27e- 97      0 NA          NA          NA          1     TRUE     NA         NA      NA         NA

> results$weights
# A tibble: 4 × 5
target           left        weight      se     z
<chr>            <chr>        <dbl>   <dbl> <dbl>
1 Italian_North.HO Steppe_EMBA 0.283  0.0230  12.3
2 Italian_North.HO Anatolia_N  0.506  0.0156  32.4
3 Italian_North.HO WHG         0.0689 0.00882  7.81
4 Italian_North.HO CHG_Iran_N  0.142  0.0264   5.38
> results$popdrop
# A tibble: 15 × 15
pat      wt   dof  chisq         p f4rank Steppe_EMBA Anatolia_N     WHG CHG_Iran_N feasible best  dofdiff chisqdiff p_nested
<chr> <dbl> <dbl>  <dbl>     <dbl>  <dbl>       <dbl>      <dbl>   <dbl>      <dbl> <lgl>    <lgl>   <dbl>     <dbl>    <dbl>
1 0000      0     7   13.5 6.03e-  2      3      0.283       0.506  0.0689     0.142  TRUE     NA         NA      NA         NA
2 0001      1     8   50.9 2.74e-  8      2      0.388       0.566  0.0458    NA      TRUE     TRUE        0     -24.0        1
3 0010      1     8   74.9 5.25e- 13      2      0.405       0.550 NA          0.0456 TRUE     TRUE        0    -251.         1
4 0100      1     8  326.  1.16e- 65      2     -0.204      NA      0.203      1.00   FALSE    TRUE        0     168.         0
5 1000      1     8  158.  4.32e- 30      2     NA           0.442  0.130      0.428  TRUE     TRUE       NA      NA         NA
6 0011      2     9   89.1 2.45e- 15      1      0.432       0.568 NA         NA      TRUE     NA         NA      NA         NA
7 0101      2     9 1415.  4.83e-299      1      1.14       NA     -0.137     NA      FALSE    NA         NA      NA         NA
8 0110      2     9  524.  4.65e-107      1     -0.0227     NA     NA          1.02   FALSE    NA         NA      NA         NA
9 1001      2     9  611.  7.94e-126      1     NA           0.815  0.185     NA      TRUE     NA         NA      NA         NA
10 1010      2     9  432.  1.69e- 87      1     NA           0.429 NA          0.571  TRUE     NA         NA      NA         NA
11 1100      2     9  421.  3.58e- 85      1     NA          NA      0.154      0.846  TRUE     NA         NA      NA         NA
12 0111      3    10 1583.  0              0      1          NA     NA         NA      TRUE     NA         NA      NA         NA
13 1011      3    10 1030.  6.62e-215      0     NA           1     NA         NA      TRUE     NA         NA      NA         NA
14 1101      3    10 1952.  0              0     NA          NA      1         NA      TRUE     NA         NA      NA         NA
15 1110      3    10  604.  2.59e-123      0     NA          NA     NA          1      TRUE     NA         NA      NA         NA