millironx/beefblup
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Push pedigree matrix to its own function

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Thomas A. Christensen II 2021-08-28 18:07:22 -05:00
parent 3782de85ac
commit a9ab1e8641
Signed by: millironx
GPG key ID: 139C07724802BC5D
2 changed files with 70 additions and 36 deletions
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95
src/BeefBLUP.jl
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@ -64,48 +64,14 @@ function beefblup(path::String, savepath::String, h2::Float64)
# Define fields to hold id values for animals and their parents
numanimals = length(data.id)
# Find the index values for animals and their parents
dam = indexin(data.dam, data.id)
sire = indexin(data.sire, data.id)
# Calculate the relationship matrix
A = additiverelationshipmatrix(data.id, data.dam, data.sire)
# Extract all of the fixed effects
fixedfx = select(data, Not([:id, :birthdate, :sire, :dam]))[:,1:end - 1]
(X, numgroups, normal, adjustedtraits) = fixedeffectmatrix(fixedfx)
# Create an empty matrix for the additive relationship matrix
A = zeros(numanimals, numanimals)
# Create the additive relationship matrix by the FORTRAN method presented by
# Henderson
for i in 1:numanimals
if !isnothing(dam[i]) && !isnothing(sire[i])
for j in 1:(i - 1)
A[j,i] = 0.5 * (A[j,sire[i]] + A[j,dam[i]])
A[i,j] = A[j,i]
end
A[i,i] = 1 + 0.5 * A[sire[i], dam[i]]
elseif !isnothing(dam[i]) && isnothing(sire[i])
for j in 1:(i - 1)
A[j,i] = 0.5 * A[j,dam[i]]
A[i,j] = A[j,i]
end
A[i,i] = 1
elseif isnothing(dam[i]) && !isnothing(sire[i])
for j in 1:(i - 1)
A[j,i] = 0.5 * A[j,sire[i]]
A[i,j] = A[j,i]
end
A[i,i] = 1
else
for j in 1:(i - 1)
A[j,i] = 0
A[i,j] = 0
end
A[i,i] = 1
end
end
# Extract the observed data
Y = convert(Array{Float64}, data[:,end])
@ -271,4 +237,61 @@ function fixedeffectmatrix(fixedeffects::AbstractDataFrame)
return X, numgroups, normal, adjustedtraits
end
"""
additiverelationshipmatrix(id, dam, sire)
Returns the additive numerator relationship matrix based on the pedigree provided in `dam`
and `sire` for animals in `id`.
"""
function additiverelationshipmatrix(id::AbstractVector, damid::AbstractVector, sireid::AbstractVector)
# Sanity-check for valid pedigree
if !(length(id) == length(damid) && length(damid) == length(sireid))
throw(ArgumentError("id, dam, and sire must be of the same length"))
end
# Convert to positions
dam = indexin(damid, id)
sire = indexin(sireid, id)
# Calculate loop iterations
numanimals = length(dam)
# Create an empty matrix for the additive relationship matrix
A = zeros(numanimals, numanimals)
# Create the additive relationship matrix by the FORTRAN method presented by
# Henderson
for i in 1:numanimals
if !isnothing(dam[i]) && !isnothing(sire[i])
for j in 1:(i - 1)
A[j,i] = 0.5 * (A[j,sire[i]] + A[j,dam[i]])
A[i,j] = A[j,i]
end
A[i,i] = 1 + 0.5 * A[sire[i], dam[i]]
elseif !isnothing(dam[i]) && isnothing(sire[i])
for j in 1:(i - 1)
A[j,i] = 0.5 * A[j,dam[i]]
A[i,j] = A[j,i]
end
A[i,i] = 1
elseif isnothing(dam[i]) && !isnothing(sire[i])
for j in 1:(i - 1)
A[j,i] = 0.5 * A[j,sire[i]]
A[i,j] = A[j,i]
end
A[i,i] = 1
else
for j in 1:(i - 1)
A[j,i] = 0
A[i,j] = 0
end
A[i,i] = 1
end
end
return A
end
end

11
test/runtests.jl
View file

@ -7,4 +7,15 @@ using Test
correctX = [1 1 0 0; 1 1 0 1; 1 0 1 0; 1 0 1 1; 1 0 1 0; 1 0 1 1; 1 0 0 0]
fixedfx = DataFrame(year = [1990, 1990, 1991, 1991, 1991, 1991, 1992], sex = ["male", "female", "male", "female", "male", "female", "male"])
@test BeefBLUP.fixedeffectmatrix(fixedfx)[1] == correctX
correctA = [1 0 1/2 1/2 1/2 0 0;
0 1 0 0 1/2 1/2 0;
1/2 0 1 1/4 1/4 0 0;
1/2 0 1/4 1 1/4 0 0;
1/2 1/2 1/4 1/4 1 1/4 0;
0 1/2 0 0 1/4 1 0;
0 0 0 0 0 0 1]
id = collect(1:7)
dam_id = [missing, missing, missing, missing, 2, 2, missing]
sire_id = [missing, missing, 1, 1, 1, missing, missing]
@test BeefBLUP.additiverelationshipmatrix(id, dam, sire) == correctA
end