Last updated: 2024-03-06
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Knit directory: HenriqueDGen/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5f808d6 | LucianoRogerio | 2023-11-30 | New Updates |
| html | 5f808d6 | LucianoRogerio | 2023-11-30 | New Updates |
suppressMessages(library(tidyverse))
suppressMessages(library(adegenet))
library(reactable)
library(here)here() starts at /Users/luciano/Documents/GitHub/HenriqueDGenlibrary(data.table)
Attaching package: 'data.table'The following objects are masked from 'package:lubridate':
hour, isoweek, mday, minute, month, quarter, second, wday, week,
yday, yearThe following objects are masked from 'package:dplyr':
between, first, lastThe following object is masked from 'package:purrr':
transposeBLUPS <- readRDS(here::here("output", "BLUPsDiseaseAgro.rds"))
rownames(BLUPS) <- BLUPS$CLONE
BLUPS2 <- BLUPS[,-1] %>% scale(., center = T, scale = T)
BLUPS[is.na(BLUPS)] <- 0
BLUPS2[is.na(BLUPS2)] <- 0BLUPS2 <- BLUPS2 %>% as.data.frame %>%
dplyr::mutate(SelIn = -10*Anth + -10*BlLS + -10*BrLS + -5*WhLS + 5*Vigor
+ 8*NR + 10*RF + 20*DRY + 10*DMC + 10*PTR + 5*PPA)
BLUPS <- BLUPS %>% mutate(SelInd = BLUPS2$SelIn)
BLUPSTest <- BLUPS[BLUPS$CLONE %in% c("BGM-1683", "BGM-2095", "BGM-2097", "BGM-2151", "BGM-2339", "BRS-Amansa-Burro",
"BRS-Caipira", "BRS-Dourada", "BRS-Formosa", "BRS-Formosa-Tetra", "BRS-Gema-de-Ovo",
"BRS-Jari", "BRS-Kiriris", "BRS-Mulatinha", "BRS-NovoHorizonte", "BRS-Poti-Branca",
"BRS-Tapioqueira", "BRS-Verdinha", "BR-11-34-41", "BR-11-34-45", "BR-11-34-64", "BR-12-107-002"),]
BLUPSGer <- BLUPS[!BLUPS$CLONE %in% BLUPSTest$CLONE,]
Top30 <- BLUPSGer %>% arrange(desc(SelInd)) %>% .[2:31,]
BLUPSF <- Top30 %>% bind_rows(BLUPSTest)
write.table(BLUPSF, file = here::here("output", "BLUPsSel.csv"), sep = ",", quote = F, row.names = F)((colMeans(Top30[,-1]) - colMeans(BLUPSTest[,-1]))/colMeans(BLUPSTest[,-1]))*100 Anth BlLS BrLS WhLS Vigor NR RF
-1.640186 -1.944298 -1.754515 -3.259334 31.334555 -10.406634 3.878786
DRY DMC PTR PPA SelInd
11.197848 8.484599 11.760792 23.667554 59.737739
sessionInfo()R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.3.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Sao_Paulo
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.15.0 here_1.0.1 reactable_0.4.4 adegenet_2.1.10
[5] ade4_1.7-22 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[9] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1
[13] tibble_3.2.1 ggplot2_3.5.0 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] gtable_0.3.4 xfun_0.42 bslib_0.6.1 htmlwidgets_1.6.4
[5] lattice_0.22-5 tzdb_0.4.0 vctrs_0.6.5 tools_4.3.2
[9] generics_0.1.3 parallel_4.3.2 fansi_1.0.6 cluster_2.1.6
[13] pkgconfig_2.0.3 Matrix_1.6-5 lifecycle_1.0.4 compiler_4.3.2
[17] git2r_0.33.0 munsell_0.5.0 permute_0.9-7 httpuv_1.6.14
[21] htmltools_0.5.7 sass_0.4.8 yaml_2.3.8 later_1.3.2
[25] pillar_1.9.0 jquerylib_0.1.4 whisker_0.4.1 seqinr_4.2-36
[29] ellipsis_0.3.2 MASS_7.3-60.0.1 cachem_1.0.8 vegan_2.6-4
[33] nlme_3.1-164 mime_0.12 tidyselect_1.2.0 digest_0.6.34
[37] stringi_1.8.3 reshape2_1.4.4 splines_4.3.2 rprojroot_2.0.4
[41] fastmap_1.1.1 grid_4.3.2 colorspace_2.1-0 cli_3.6.2
[45] magrittr_2.0.3 utf8_1.2.4 ape_5.7-1 withr_3.0.0
[49] scales_1.3.0 promises_1.2.1 timechange_0.3.0 rmarkdown_2.25
[53] igraph_2.0.2 workflowr_1.7.1 hms_1.1.3 shiny_1.8.0
[57] evaluate_0.23 knitr_1.45 mgcv_1.9-1 rlang_1.1.3
[61] Rcpp_1.0.12 xtable_1.8-4 glue_1.7.0 rstudioapi_0.15.0
[65] jsonlite_1.8.8 R6_2.5.1 plyr_1.8.9 fs_1.6.3