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Mvp updates #84

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merged 2 commits into from
Dec 20, 2024
Merged

Mvp updates #84

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c586efd
Merge pull request #83 from Breeding-Insight/development
alex-sandercock Dec 20, 2024
9813e52
GS and UI updates
alex-sandercock Dec 20, 2024
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4 changes: 2 additions & 2 deletions R/GS_functions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -311,9 +311,9 @@ GBLUP_genomic_prediction <- function(pheno_dat, Geno.mat, cycles, folds, traits,
results[(((r-1)*5)+fold), (length(traits)+2)] <- fold

# Extract GEBVs
GEBVs_fold[, trait_idx] <- traitpred$g[test] #Confirm it is accuract to calculate the GEBVs for testing group from the trained model
GEBVs_fold[, trait_idx] <- traitpred$g[test]

# Calculate heritability (these are wrong)
# Calculate heritability (*confirm this calculation* - either way will not report to user)
Vu <- traitpred$Vg
Ve <- traitpred$Ve
heritability_scores[(((r-1)*5)+fold), trait_idx] <- Vu / (Vu + Ve)
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2 changes: 1 addition & 1 deletion R/app_ui.R
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Expand Up @@ -57,7 +57,7 @@ app_ui <- function(request) {
menuItem("Home", tabName = "welcome", icon = icon("house"),startExpanded = FALSE),
tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Genotype Processing"),
menuItem("Convert to VCF", tabName = "dosage2vcf", icon = icon("share-from-square")),
menuItem("Updog Dosage Calling", tabName = "updog", icon = icon("list-ol")),
menuItem("Dosage Calling", tabName = "updog", icon = icon("list-ol")),
menuItem("VCF Filtering", tabName = "filtering", icon = icon("filter")),
tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Summary Metrics"),
menuItem("Genomic Diversity", tabName = "diversity", icon = icon("chart-pie")),
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4 changes: 2 additions & 2 deletions R/mod_Filtering.R
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Expand Up @@ -40,9 +40,9 @@ mod_Filtering_ui <- function(id){
numericInput(ns("maxpostprob_filter"), "Minimum maxpostprob (Updog filter)", min = 0, value = 0.5, step = 0.1)
)
),
actionButton(ns("run_filters"), "Apply filters"),
actionButton(ns("run_filters"), "Apply Filters"),
useShinyjs(),
downloadButton(ns("start_updog_filter"), "Download Filtered VCF", icon = icon("download"), class = "butt"),
downloadButton(ns("start_updog_filter"), "Download", icon = icon("download"), class = "butt"),
div(style="display:inline-block; float:right",dropdownButton(
tags$h3("Updog Filter Parameters"),
"You can download examples of the expected file here: \n",
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