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uqrmaie1 / admixtools

https://uqrmaie1.github.io/admixtools
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Error in parse_qpadm_output #53

Open jaurbanChicago opened 9 months ago

jaurbanChicago commented 9 months ago

Hi Robert,

There is an error in the parse_qpadm_output command because the command is printing the weights again in the se column in $weights.

> test                                                                                                             
$weights
# A tibble: 3 x 6
  target         left                weight  mean    se     z
  <chr>          <chr>                <dbl> <dbl> <dbl> <dbl>
1 STUHG03645_KGP IPC                  0.522 0.522 0.522     1
2 STUHG03645_KGP Onge                 0.386 0.386 0.386     1
3 STUHG03645_KGP Central_Steppe_MLBA  0.092 0.092 0.092     1

$popdrop
# A tibble: 7 x 9
  pat      wt   dof  chisq        p   IPC  Onge Central_Steppe_MLBA feasible
  <chr> <dbl> <dbl>  <dbl>    <dbl> <dbl> <dbl>               <dbl> <lgl>   
1 000       0     5   11.1 4.88e- 2 0.522 0.386               0.092 TRUE    
2 001       1     6   21.4 1.53e- 3 0.644 0.356               0     TRUE    
3 010       1     6  204.  0        1.11  0                  -0.113 FALSE   
4 100       1     6  148.  2.54e-29 0     0.632               0.368 TRUE    
5 011       2     7  219.  0        1     0                   0     TRUE    
6 101       2     7  517.  0        0     1                   0     TRUE    
7 110       2     7 1574.  0        0     0                   1     TRUE

Best

uqrmaie1 commented 6 months ago

Sorry, I missed that. I can't reproduce the problem. Can you share the qpAdm output file?