Last updated: 2020-12-04
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Knit directory: IITA_2020GS/
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| Rmd | 9718666 | wolfemd | 2020-12-03 | Refresh BLUPs and GBLUPs with trials harvested so far. Include |
# activate multithread OpenBLAS
export OMP_NUM_THREADS=44library(tidyverse)
library(magrittr)
source(here::here("code", "gsFunctions.R"))
A <- readRDS(file = here::here("output", "Kinship_A_IITA_2020Sep16.rds"))
D <- readRDS(file = here::here("output", "Kinship_D_IITA_2020Sep16.rds"))
AD <- readRDS(file = here::here("output", "Kinship_AD_IITA_2020Sep16.rds"))
# BLUPs from the 2 stage procedure (stage 1 of 2) using the 2019 procedure
blups <- readRDS(file = here::here("output", "iita_blupsForModelTraining_twostage_asreml_2020Dec03.rds")) %>%
dplyr::select(Trait, blups) %>% unnest(blups) %>% filter(GID %in% rownames(A)) %>%
nest(TrainingData = -Trait)cbsurobbins (112 cores; 512GB)
Model ADE
options(future.globals.maxSize = 3000 * 1024^2)
predModelADE <- runGenomicPredictions(blups, modelType = "ADE", grms = list(A = A,
D = D, AD = AD), gid = "GID", ncores = 14)
saveRDS(predModelADE, file = here::here("output", "genomicPredictions_ModelADE_twostage_IITA_2020Dec03.rds"))library(tidyverse); library(magrittr);
predModelADE<-readRDS(file = here::here("output","genomicPredictions_ModelADE_twostage_IITA_2020Dec03.rds"))
traits<-c("MCMDS","DM","PLTHT","BRNHT1","BRLVLS","HI",
"logDYLD", # <-- logDYLD now included.
"logFYLD","logTOPYLD","logRTNO","TCHART","LCHROMO","ACHROMO","BCHROMO")## Format and write GETGV
predModelADE %>% dplyr::select(Trait, genomicPredOut) %>% unnest(genomicPredOut) %>%
select(-varcomps) %>% unnest(gblups) %>% select(Trait, GID, GETGV) %>% spread(Trait,
GETGV) %>% mutate(GeneticGroup = NA, GeneticGroup = ifelse(grepl("TMS18", GID,
ignore.case = T), "TMS18", ifelse(grepl("TMS15", GID, ignore.case = T), "TMS15",
ifelse(grepl("TMS14", GID, ignore.case = T), "TMS14", ifelse(grepl("TMS13|2013_",
GID, ignore.case = T), "TMS13", "GGetc"))))) %>% select(GeneticGroup, GID,
any_of(traits)) %>% arrange(desc(GeneticGroup)) %>% write.csv(., file = here::here("output",
"GETGV_IITA_ModelADE_twostage_IITA_2020Dec03.csv"), row.names = F)
sessionInfo()R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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
other attached packages:
[1] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 whisker_0.4 knitr_1.30 magrittr_2.0.1
[5] R6_2.5.0 rlang_0.4.9 stringr_1.4.0 tools_4.0.2
[9] xfun_0.19 git2r_0.27.1 htmltools_0.5.0 ellipsis_0.3.1
[13] yaml_2.2.1 digest_0.6.27 rprojroot_2.0.2 tibble_3.0.4
[17] lifecycle_0.2.0 crayon_1.3.4 formatR_1.7 later_1.1.0.1
[21] vctrs_0.3.5 promises_1.1.1 fs_1.5.0 glue_1.4.2
[25] evaluate_0.14 rmarkdown_2.5 stringi_1.5.3 compiler_4.0.2
[29] pillar_1.4.7 httpuv_1.5.4 pkgconfig_2.0.3