Last updated: 2022-08-18
Checks: 6 1
Knit directory: IITA_2022GS/
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Follow outlined GenomicPredictionChecklist and previous pipeline to process cassavabase data for ultimate genomic prediction.
Below we will clean and format training data.
Downloaded all NRCRI field trials.
Selected all IITA trials currently available. Make a list. Named it IITATrials2022GS.
Go to Manage –> Download here. Download phenotypes (plot-basis only) and meta-data as CSV using the corresponding boxes / drop-downs.
Store flatfiles, in directory data/:
- 2022-07-27T091701phenotype_download.csv
- 2022-07-27T093145metadata_download.csv
sessionInfo()R version 4.1.3 (2022-03-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.6.8
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 rstudioapi_0.13 knitr_1.39 magrittr_2.0.3
[5] workflowr_1.7.0 R6_2.5.1 rlang_1.0.3 fastmap_1.1.0
[9] fansi_1.0.3 stringr_1.4.0 tools_4.1.3 xfun_0.31
[13] utf8_1.2.2 cli_3.3.0 git2r_0.30.1 jquerylib_0.1.4
[17] htmltools_0.5.2 ellipsis_0.3.2 rprojroot_2.0.3 yaml_2.3.5
[21] digest_0.6.29 tibble_3.1.7 lifecycle_1.0.1 crayon_1.5.1
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[29] fs_1.5.2 glue_1.6.2 evaluate_0.15 rmarkdown_2.14
[33] stringi_1.7.6 bslib_0.3.1 compiler_4.1.3 pillar_1.7.0
[37] jsonlite_1.8.0 httpuv_1.6.5 pkgconfig_2.0.3