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mcanouil / eggla

Early Growth Genetics Longitudinal Analysis
https://m.canouil.dev/eggla/
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INFO_TYPE description given to genotyped SNPs #86

Closed annihei closed 1 year ago

annihei commented 1 year ago

Bug description

This is related to the previous issue #80 I reported, turned out I didn't check the results carefully enough. So I was able to run run_eggla_gwas with R2 in the INFO, but the description given in the function argument info_type went only to genotyped SNPs.

P.S. Sorry for taking time with the analysis plan, I am trying to learn how to respond to the review request!

eggla version output

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Locale:
  LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
  LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
  LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
  LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

Package version:
  backports_1.4.1      bayestestR_0.13.0    beeswarm_0.4.0      
  BH_1.75.0.0          bit_4.0.4            bit64_4.0.5         
  broom_1.0.1          broom.mixed_0.2.9.4  cli_3.4.1           
  clipr_0.8.0          coda_0.19.4          codetools_0.2.18    
  colorspace_2.0.3     compiler_4.2.1       cpp11_0.4.3         
  crayon_1.5.2         curl_4.3.3           data.table_1.14.4   
  datawizard_0.6.3     digest_0.6.30        distributional_0.3.1
  doParallel_1.0.17    dplyr_1.0.10         eggla_0.17.4        
  ellipsis_0.3.2       fansi_1.0.3          farver_2.1.1        
  forcats_0.5.2        foreach_1.5.2        furrr_0.3.1         
  future_1.28.0        generics_0.1.3       ggbeeswarm_0.6.0    
  ggdist_3.2.0         ggplot2_3.3.6        ggtext_0.1.2        
  globals_0.16.1       glue_1.6.2           graphics_4.2.1      
  grDevices_4.2.1      grid_4.2.1           gridtext_0.1.5      
  growthcleanr_2.0.0   gtable_0.3.1         haven_2.5.1         
  HDInterval_0.2.2     hms_1.1.2            insight_0.18.6      
  isoband_0.2.6        iterators_1.0.14     jpeg_0.1.9          
  labeling_0.4.2       labelled_2.10.0      lattice_0.20.44     
  lifecycle_1.0.3      listenv_0.8.0        magrittr_2.0.3      
  markdown_1.2         MASS_7.3.53          Matrix_1.3.3        
  methods_4.2.1        mgcv_1.8.35          mime_0.12           
  munsell_0.5.0        nlme_3.1.152         numDeriv_2016.8.1.1 
  parallel_4.2.1       parallelly_1.32.1    patchwork_1.1.2     
  performance_0.10.0   pillar_1.8.1         pkgconfig_2.0.3     
  plyr_1.8.7           png_0.1.7            prettyunits_1.1.1   
  progress_1.2.2       purrr_0.3.5          R6_2.5.1            
  RColorBrewer_1.1.3   Rcpp_1.0.9           readr_2.1.3         
  rlang_1.0.6          scales_1.2.1         splines_4.2.1       
  stats_4.2.1          stringi_1.7.8        stringr_1.4.1       
  tibble_3.1.8         tidyr_1.2.1          tidyselect_1.2.0    
  tools_4.2.1          tzdb_0.3.0           utf8_1.2.2          
  utils_4.2.1          vctrs_0.5.0          vipor_0.4.5         
  viridisLite_0.4.1    vroom_1.6.0          withr_2.5.0         
  xfun_0.34            xml2_1.3.3

Checklist

mcanouil commented 1 year ago

I will check, I might have get the condition the wrong way. It should be an easy/quick fix.

mcanouil commented 1 year ago

@annihei Are you sure? From my code, for all variants with R2/INFO different from 1, the info_type is added. See https://github.com/mcanouil/eggla/blob/main/R/run_eggla_gwas.R#L534-L563.

Never mind, I saw where the condition was off.

mcanouil commented 1 year ago

v0.18.1 will be available soon with the fix. Thanks for noticing and reporting this.

mcanouil commented 1 year ago

@annihei @burrowsk v0.18.1 is available. The Docker image and the updated documentation website will be online within the next hour.

annihei commented 1 year ago

Thanks!