Last updated: 2023-10-27

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Knit directory: Genomic-Selection-for-Drought-Tolerance-Using-Genome-Wide-SNPs-in-Casava/

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html 90dc112 WevertonGomesCosta 2022-11-17 Update
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Rmd 5988c27 WevertonGomesCosta 2022-11-11 Update
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Rmd b78c842 WevertonGomesCosta 2022-10-20 Start workflowr project.

This website is a project for analysis of the Genomic Selection for Drought Tolerance Using Genome-Wide GBS and/or DART in Cassava by EMBRAPA Cassava.

In this project, you will find how the estimation of BLUPs was performed using mixed models. In addition, we performed the EDA and some manipulations were necessary to estimate the BLUPs.

For the GWS, we used the original marker matrix. Thus, we also had to perform some manipulations to organize and prepare the matrix for input into the models. The models used were RR-BLUP and G-BLUP. Finally, we performed cross-validation only for the G-BLUP, since the results were similar for both methods.


sessionInfo()
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=Portuguese_Brazil.utf8  LC_CTYPE=Portuguese_Brazil.utf8   
[3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C                      
[5] LC_TIME=Portuguese_Brazil.utf8    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.11       rstudioapi_0.15.0 whisker_0.4.1     knitr_1.44       
 [5] magrittr_2.0.3    workflowr_1.7.1   R6_2.5.1          rlang_1.1.1      
 [9] fastmap_1.1.1     fansi_1.0.4       stringr_1.5.0     tools_4.2.3      
[13] xfun_0.40         utf8_1.2.3        cli_3.6.1         git2r_0.32.0     
[17] jquerylib_0.1.4   htmltools_0.5.6   rprojroot_2.0.3   yaml_2.3.7       
[21] digest_0.6.33     tibble_3.2.1      lifecycle_1.0.3   later_1.3.1      
[25] sass_0.4.7        vctrs_0.6.3       promises_1.2.1    fs_1.6.3         
[29] cachem_1.0.8      glue_1.6.2        evaluate_0.22     rmarkdown_2.25   
[33] stringi_1.7.12    bslib_0.5.1       compiler_4.2.3    pillar_1.9.0     
[37] jsonlite_1.8.7    httpuv_1.6.11     pkgconfig_2.0.3

  1. Weverton Gomes da Costa, Pós-Doutorando, Embrapa Mandioca e Fruticultura, ↩︎