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Correct extract_selections.R #1

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10 changes: 5 additions & 5 deletions R/extract_selections.R
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Original file line number Diff line number Diff line change
Expand Up @@ -61,17 +61,17 @@ extract_selections <- function(num.cores=NULL, map.info, cross.design, past.tgv,
map.markers$chr <- as.character(map.markers$chr)

# Generate pedigree using synbreed if 1st generation otherwise just use full.ped object
# Create 2 objects which hold all markers and all phenotypes respectively
# Create 2 objects which hold all markers and all phenotypes respectively ##** NOTE: synbreed is not loaded, pedigreemm is.

if (generation==1) {
ped <- pedigree::pedigree(label = full.ped[,1],sire = full.ped[,2],dam = full.ped[,3])
ped <- pedigreemm::pedigree(label = full.ped[,1],sire = full.ped[,2],dam = full.ped[,3])
#all.markers <- rbind(parent.markers,)
if(reduced){ all.phenos <- c(parent.info$phenos,progeny.phenos)
all.genetic.vals <- c(parent.info$genetic.values,prog.genetic.values)
} else { all.phenos <- c(past.phenos$phenos,progeny.phenos)
all.genetic.vals <- c(past.phenos$genetic.values,prog.genetic.values)}
} else {
ped <- pedigree::pedigree(label = selection.ped[,1],sire = selection.ped[,2],dam = selection.ped[,3])
ped <- pedigreemm::pedigree(label = selection.ped[,1],sire = selection.ped[,2],dam = selection.ped[,3])
#all.markers <- rbind(parent.markers,prog.markers)
all.phenos <- c(parent.info$all.phenos,progeny.phenos)
all.genetic.vals <- c(past.phenos$genetic.values,prog.genetic.values)
Expand Down Expand Up @@ -532,7 +532,7 @@ extract_selections <- function(num.cores=NULL, map.info, cross.design, past.tgv,
# Calculate:
# Inbreding level of progeny/selections
# Genetic Variance of progeny and selections (Bulmer Effect)
f.ped <- pedigree::pedigree(label = full.ped[,1],sire = full.ped[,2],dam = full.ped[,3])
f.ped <- pedigreemm::pedigree(label = full.ped[,1],sire = full.ped[,2],dam = full.ped[,3])
pedigree.inbreeding <- pedigreemm::inbreeding(f.ped)
names(pedigree.inbreeding) <- full.ped[,1]
progeny.inbreeding <- pedigree.inbreeding[prog.pedigree[,1]]
Expand All @@ -549,7 +549,7 @@ extract_selections <- function(num.cores=NULL, map.info, cross.design, past.tgv,
if(generation == 1){A <- as.matrix(pedigreemm::getA(f.ped))
} else {
selection.ped <- cross.design$selection.ped
s.ped <- pedigree::pedigree(label = selection.ped[,1],sire = selection.ped[,2],dam = selection.ped[,3])
s.ped <- pedigreemm::pedigree(label = selection.ped[,1],sire = selection.ped[,2],dam = selection.ped[,3])
A <- as.matrix(pedigreemm::getA(s.ped))}
l <- match(names(selection.phenos), rownames(A))
rel.mat <- A[l,l]
Expand Down