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Fixed lookups for additive relationship matrix

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Thomas A. Christensen II 2018-09-27 22:29:34 -06:00
parent 88fbf16ed4
commit bd44916781
1 changed files with 23 additions and 15 deletions
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38
MATLAB/beefblup.m
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@ -32,7 +32,8 @@ data(:,strings) = cellfun(@num2str, data(:,strings), 'UniformOutput', false);
% Create a lookup lambda function to find the animal represented by a
% certain id
animalrow = @(id) find(strcmp(data(:,1), id));
animal2row = @(id) find(strcmp(data(:,1), id));
row2animal = @(rownum) [data{rownum,1}];
ids = [data{:,1}];
numanimals = length(data(:,1));
@ -132,13 +133,20 @@ end
A = zeros(numanimals, numanimals);
% Create lambdas to find sire and dam of each animal
dam = @(id) [data{animalrow(num2str(id)), 3}];
sire = @(id) [data{animalrow(num2str(id)), 4}];
id2dam = @(id) [data{animal2row(num2str(id)), 3}];
id2sire = @(id) [data{animal2row(num2str(id)), 4}];
row2dam = @(rownum) [data{rownum, 3}];
row2sire = @(rownum) [data{rownum, 4}];
rowofdam = @(id) animal2row(id2dam(id));
rowofsire = @(id) animal2row(id2sire(id));
row2rowofdam = @(rownum) rowofdam(row2animal(rownum));
row2rowofsire = @(rownum) rowofsire(row2animal(rownum));
% Create the additive relationship matrix by the FORTRAN method presented
% by Henderson
for i = 1:numanimals
if strcmp(sire(i), 'NaN') && strcmp(dam(i), 'NaN')
id = row2animal(i);
if isempty(row2rowofsire(i)) && isempty(row2rowofdam(i))
for j = 1:(i-1)
A(j,i) = 0;
end
@ -146,29 +154,29 @@ for i = 1:numanimals
continue
end
if strcmp(sire(i), 'NaN') && not(strcmp(dam(i), 'NaN'))
if isempty(row2rowofsire(i)) && not(isempty(row2dam(i)))
for j = 1:(i-1)
A(j,i) = A(j,str2double(dam(i)));
A(i,j) = A(j,str2double(dam(i)));
A(j,i) = A(j,row2rowofdam(i));
A(i,j) = A(j,row2rowofdam(i));
end
A(i,i) = 1;
continue
end
if strcmp(dam(i), 'NaN') && not(strcmp(sire(i), 'NaN'))
if isempty(row2rowofdam(i)) && not(isempty(row2rowofsire(i)))
for j=1:(i-1)
A(j,i) = A(j,str2double(sire(i)));
A(i,j) = A(j,str2double(sire(i)));
A(j,i) = A(j,row2rowofsire(i));
A(i,j) = A(j,row2rowofsire(i));
end
A(i,i) = 1;
continue
end
for j=1:(i-1)
A(j,i) = 0.5.*(A(j,str2double(sire(i))) + A(j,str2double(dam(i))));
A(i,j) = 0.5.*(A(j,str2double(sire(i))) + A(j,str2double(dam(i))));
A(j,i) = 0.5.*(A(j,row2rowofsire(i)) + A(j,row2rowofdam(i)));
A(i,j) = 0.5.*(A(j,row2rowofsire(i)) + A(j,row2rowofdam(i)));
end
A(i,i) = 1 + 0.5.*A(str2double(sire(i)), str2double(dam(i)));
A(i,i) = 1 + 0.5.*A(row2rowofsire(i), row2rowofdam(i));
continue
end
@ -179,8 +187,8 @@ Y = cell2mat(data(:, 5));
% The identity matrix for random effects
Z = eye(numanimals, numanimals);
% Prompt for heritablity
h2 = input('What is the heritablity for this trait? >> ');
% Prompt for heritability
h2 = input('What is the heritability for this trait? >> ');
lambda = (1-h2)/h2;
% Use the mixed-model equations