Admixtools 2

[TanTin]

I think I notices some bad bug in Admixtools 2 for group statistics.  
(  from  library("admixtools"))

Running the same test for the same groups: I got different results for each run.
It doesn't make much sense , unless if there is some random algorithm for simplification of calculations.


Test population:

TEST
[1] "Turkey_N"                        "Iran_GanjDareh_N"                "Georgia_Kotias.SG"              "Russia_Sidelkino_HG.SG"       
[5] "Tajikistan_BA_DashtiKozy"        "Greece_Minoan_Lassithi"          "Greece_Minoan_Kephala_Petras.SG" "Greece_Minoan_Odigitria"       
[9] "Italy_South_HG_Ostuni2"          "Russia_Ust_Ishim.DG"            "Denisova.DG"                    "Vindija_Neanderthal.DG"       
[13] "Papuan.SDG"                      "Greece_BA_Mycenaean_Pylos"      "Greece_BA_Mycenaean"            "Micronesia_Pohnpei_400BP"     
[17] "Chimp.REF"                      "JPT.SG"                          "Mongolia_Salkhit_UP.SG"          "Japan_HG_Jomon"               
>



This is the test:



f4( prefix,  TEST ,  "Russia_Ust_Ishim.DG",  "Denisova.DG" ,  "Vindija_Neanderthal.DG" )  #
prefix -> is the path to the dataset  v52.2_1240K   :  in my case in another subfolder:
"../v52.2/geno/v52.2_1240K_public"

To run the test just execute the command in R:   f4( prefix,  TEST ,  "Russia_Ust_Ishim.DG",  "Denisova.DG" ,  "Vindija_Neanderthal.DG" )

This is the activity log in real time:

i Getting population combinations...
i 20 population combinations found
i Computing from f4 from genotype data...
i Reading metadata...
i Computing block lengths for 1150639 SNPs...
i Computing 20 f4-statistics for block 713 out of 713...
i Summarize across blocks...


Next: the results:

Show Content

Spoiler
# A tibble: 20 x 9
  pop1                            pop2                pop3        pop4                          est      se      z          p      n
  <chr>                          <chr>              <chr>      <chr>                      <dbl>    <dbl>  <dbl>      <dbl>  <dbl>
1 Turkey_N                        Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.00157  0.000346  -4.53    5.97e-  6 1005076
2 Iran_GanjDareh_N                Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG  0.000298  0.000218  1.37    1.71e-  1  961681
3 Georgia_Kotias.SG              Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG  0.000219  0.000247  0.886  3.75e-  1 1010220
4 Russia_Sidelkino_HG.SG          Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.000152  0.000271  -0.563  5.74e-  1  873308
5 Tajikistan_BA_DashtiKozy        Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.000132  0.000202  -0.651  5.15e-  1  913838
6 Greece_Minoan_Lassithi          Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG  0.000140  0.000212  0.663  5.07e-  1  894038
7 Greece_Minoan_Kephala_Petras.SG Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG  0.0000310 0.000234  0.132  8.95e-  1 1000258
8 Greece_Minoan_Odigitria        Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.000182  0.000376  -0.484  6.28e-  1  274463
9 Italy_South_HG_Ostuni2          Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.000853  0.00199  -0.429  6.68e-  1    8797
10 Russia_Ust_Ishim.DG            Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG  0        0        NaN    NaN        1012212
11 Denisova.DG                    Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG  0.0373    0.00123  30.5    7.57e-204 1012212
12 Vindija_Neanderthal.DG          Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.0465    0.00205  -22.7    6.61e-114 1012212
13 Papuan.SDG                      Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.00623  0.00132  -4.74    2.16e-  6 1008381
14 Greece_BA_Mycenaean_Pylos      Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG  0.000674  0.000585  1.15    2.49e-  1  159773
15 Greece_BA_Mycenaean            Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG  0.000551  0.000453  1.22    2.24e-  1  264072
16 Micronesia_Pohnpei_400BP        Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.00757  0.00141  -5.38    7.34e-  8  931290
17 Chimp.REF                      Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.0165    0.00451  -3.66    2.51e-  4  907022
18 JPT.SG                          Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.00283  0.000559  -5.06    4.09e-  7 1012211
19 Mongolia_Salkhit_UP.SG          Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.00113  0.000904  -1.25    2.11e-  1  78932
20 Japan_HG_Jomon                  Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.0000677 0.000213  -0.318  7.50e-  1  894525

[TanTin]

However the problem is that each time I run the same script for the same test populations  , I get different results. 






next run:

[TanTin]

Now, I am adding additional option for  allsnps = T , which seems to be active by default.

So the script is:
f4( prefix,  TEST ,  "Russia_Ust_Ishim.DG",  "Denisova.DG" ,  "Vindija_Neanderthal.DG" ) 

[TanTin]

I just restarted R-Studio. And rerun the previous test:





This time the numbers for the snips ( the last column) are stable,  same numbers . However the est , se and Z are still very different.  Z= est/se .

Some numbers are the same in both runs.  And the difference for some groups is very bad.  I don't see any explanation unless some bug.

[TanTin]

another version

[TanTin]

I can assure you that F4 functions work perfect if you run these on individuals (instead of  group populations).
When running F4 functions for individuals only we get the same reliable results on each run.  No such random discrepancy that I show above with the groups.
Here is such example:

Show Content

Spoiler

> cluster_data[1:20,]
# A tibble: 20 x 9
  pop1                      pop2        pop3        pop4                  est      se      z          p      n
  <chr>                    <chr>        <chr>        <chr>                <dbl>    <dbl>  <dbl>      <dbl>  <dbl>
1 tai002_noUDG.SG          Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.000915 0.000701  1.31  1.92e-  1  77860
2 Gorilla.REF              Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.0169  0.000454  37.1    1.34e-301 520864
3 Gorilla                  Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.0167  0.000459  36.3    8.54e-289 502768
4 Chimp_HO                  Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.0182  0.000451  40.5    0        560121
5 Chimp.REF                Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.0182  0.000446  40.8    0        548547
6 AltaiNeanderthal.DG      Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.0461  0.000575 -80.2    0        560059
7 AltaiNeanderthal_snpAD.DG Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.0462  0.000576 -80.2    0        560059
8 Chagyrskaya_noUDG.SG      Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.0500  0.000577 -86.5    0        560072
9 Denisova11_noUDG.SG      Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.00595  0.000474  12.6    3.65e- 36 426334
10 Goyet_noUDG.SG            Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.0510  0.000596 -85.6    0        435769
11 Les_Cottes_noUDG.SG      Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.0494  0.000579 -85.3    0        445990
12 Mezmaiskaya2_noUDG.SG    Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.0483  0.000600 -80.5    0        406983
13 Spy_noUDG.SG              Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.0487  0.000642 -75.8    0        256947
14 Vindija_snpAD.DG          Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.0559  0.000582 -96.0    0        560121
15 VindijaG1_noUDG.SG        Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.0521  0.000597 -87.3    0        338821
16 HGDP00545                Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.00212  0.000367  5.78  7.26e-  9 559695
17 I3921_noUDG              Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.00178  0.000379  4.69  2.77e-  6 512697
18 VK551_noUDG.SG            Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.000499 0.000350  1.43  1.54e-  1 474692
19 Loschbour.DG              Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.000498 0.000334  1.49  1.36e-  1 554841
20 Ust_Ishim.DG              Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0        0        NaN    NaN        560121
> cluster_data[21: length(myData$famInd ),]
# A tibble: 14 x 9
  pop1              pop2        pop3        pop4                    est      se        z      p      n
  <chr>            <chr>        <chr>        <chr>                  <dbl>    <dbl>    <dbl>  <dbl>  <dbl>
1 salkhit1_noUDG.SG Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.000685  0.000747  -0.917  0.359    76629
2 Denisova3.DG      Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.0652    0.000607 107.      0      560121
3 Tianyuan          Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.000317  0.000382  0.831  0.406  489100
4 BK-1653_noUDG    Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.00000239 0.000380  0.00629 0.995  522874
5 BB7-240_noUDG    Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.000693  0.000439  -1.58    0.114  447438
6 F6-620_noUDG      Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.000447  0.000405  -1.10    0.270  538749
7 Yana_old_noUDG.SG Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.000424  0.000338  1.25    0.210  559996
8 Kostenki14        Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.000571  0.000360  1.59    0.113  552582
9 Sunghir3_noUDG.SG Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.000660  0.000354  1.86    0.0625  559548
10 Oase1_d          Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG -0.00198    0.000633  -3.13    0.00173 115573
11 ZKU002_noUDG.SG  Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.000300  0.000370  0.810  0.418  545032
12 KK1_noUDG.SG      Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.000671  0.000350  1.92    0.0550  558972
13 SATP_noUDG.SG    Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.000761  0.000375  2.03    0.0428  333318
14 S_Iranian-2.DG    Ust_Ishim.DG Denisova3.DG Vindija_snpAD.DG  0.000514  0.000308  1.67    0.0953  554555

[TanTin]

Here are the F4- results when we run the test for Individuals ( not groups).



F4- stats for the individuals are perfectly matching to what we know already.  There is 1 special case: Salkhit.   It is on the Neanderthal side, so she is more Neanderthal than Ust-Ishim.

[AimSmall]

I don't know the cause of your random results, be curious if the original version has the same behavior.

https://uqrmaie1.github.io/admixtools/ar...nd-qpdstat
The "f4mode = FALSE" seems interesting.

Search the word "Random"
https://uqrmaie1.github.io/admixtools/ar...stats.html

Your source code is here...
https://github.com/uqrmaie1/admixtools/b.../qpdstat.R

[TanTin]

I don't know the cause of your random results, be curious if the original version has the same behavior.

https://uqrmaie1.github.io/admixtools/ar...nd-qpdstat
The "f4mode = FALSE" seems interesting.

Search the word "Random"
https://uqrmaie1.github.io/admixtools/ar...stats.html

Your source code is here...
https://github.com/uqrmaie1/admixtools/b.../qpdstat.R

I am using ‘admixtools’ version 2.0.0. 

In general I don't need and I don't use F4 for populations.  It is used in many official publications, but I don't use it. The only reason to test something  with the groups is to validate some results that I already have by using PCA or other tests.. I prefer to run F4 stats for individuals . 

To run F4 for individuals is a little bit tricky.  Because I have to modify .ind or .fam file  and to replace the group ID with the individual ID.
Running F4 for the groups is  the easy and lazy way for using Admixtools. 
However with the latest tests that I provided above: it makes nonsense to do such group tests, as these results are not reliable at all. Of course someone may play with the settings. 
For example by using:  allsnps = F option  it may fix the random results and we may get stable results, but  it will restrict the number of snips.   In the example that I provided  when  allsnps = F  I get only 94 snips included in the results. 
For qpWave and qpAdm - I know it is using some algorithms  that may create different results even if we apply the same criteria.  I did not expect that same could be true for the group F4 stats.

[AimSmall]

Everything I posted was Admixtools 2.0.

   

[kolompar]

Is this with a merged/converted dataset? That's where I've had this before, but don't know what it is that goes wrong.

[TanTin]

Is this with a merged/converted dataset? That's where I've had this before, but don't know what it is that goes wrong.

I guess this is a bug in Admixtools2.  Doesn't matter what dataset we use. We should get the same or near the same results if we specify the same criteria. 
But as we see: running the same script - same options - the results are disaster.
This is only for groups statistics.
When I run F4 on individuals I get perfect and stable results.
The bug is definately in Admixtools.
Thanks for confirming that you already have seen that.

[Арсен]

Is this with a merged/converted dataset? That's where I've had this before, but don't know what it is that goes wrong.

I guess this is a bug in Admixtools2.  Doesn't matter what dataset we use. We should get the same or near the same results if we specify the same criteria. 
But as we see: running the same script - same options - the results are disaster.
This is only for groups statistics.
When I run F4 on individuals I get perfect and stable results.
The bug is definately in Admixtools.
Thanks for confirming that you already have seen that.

dude, teach me how to use this program, question, do I have to download heavy bam ENA files from data library sites for this? and do you need a serious, powerful processor to calculate mixtures?

[TanTin]

Is this with a merged/converted dataset? That's where I've had this before, but don't know what it is that goes wrong.

I guess this is a bug in Admixtools2.  Doesn't matter what dataset we use. We should get the same or near the same results if we specify the same criteria. 
But as we see: running the same script - same options - the results are disaster.
This is only for groups statistics.
When I run F4 on individuals I get perfect and stable results.
The bug is definately in Admixtools.
Thanks for confirming that you already have seen that.

dude, teach me how to use this program, question, do I have to download heavy bam ENA files from data library sites for this? and do you need a serious, powerful processor to calculate mixtures?

There is already such topic in Eupedia. Start from there.

https://www.eupedia.com/forum/threads/ad...ows.42684/

Regarding converting converting  bam to plink format - this is another topic. It is a different process. For now try to make your software working with the already available data. (in plink bed,bim fam  format).

[Арсен]

I guess this is a bug in Admixtools2.  Doesn't matter what dataset we use. We should get the same or near the same results if we specify the same criteria. 
But as we see: running the same script - same options - the results are disaster.
This is only for groups statistics.
When I run F4 on individuals I get perfect and stable results.
The bug is definately in Admixtools.
Thanks for confirming that you already have seen that.

dude, teach me how to use this program, question, do I have to download heavy bam ENA files from data library sites for this? and do you need a serious, powerful processor to calculate mixtures?

There is already such topic in Eupedia. Start from there.

https://www.eupedia.com/forum/threads/ad...ows.42684/

Regarding converting converting  bam to plink format - this is another topic. It is a different process. For now try to make your software working with the already available data. (in plink bed,bim fam  format).

nothing is clear but very interesting xD