The first example is the Myostatin genes and are taken from the paper.
We will include a matlab script file called data_dna.m to initialize the data.
Below we demonstrate how the pairwise distances for the DNA profiles may be computed using the matlab interpreter
The end result are pairwise distance matrices LED, L1D, L2D, and LinfD which are the distances measured with the various norms.
The Entropy distance norm is computed with the e02daug( *, * ) function call.
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Y = data_dna();
for e = 1:max(size( Y))
for ee = (e+1):max(size( Y))
if ( norm( Y(:,e) - Y(:,ee) ) > eps )
[d, L , E, PErr ] = e02daug(Y(:,e),Y(:,ee)) ;
else
d = 0;
end
EDd(e,ee)=d ;
end
end
for e = 1:max(size( Y))
for ee = e:max(size( Y))
L2D(e,ee) = norm( Y(:,e) - Y(:,ee) ,2 )
end
end
for e = 1:max(size( Y))
for ee = e:max(size( Y))
L1D(e,ee) = norm( Y(:,e) - Y(:,ee) ,1 )
end
end
for e = 1:max(size( Y))
for ee = e:max(size( Y))
LinfD(e,ee) = norm( Y(:,e) - Y(:,ee) ,inf )
end
end
LED = zeros( max(size( Y)) )
LED(1:7,:) = EDd;
LED = LED + LED';
L1D = L1D + L1D';
LinfD = LinfD + LinfD';
L2D = L2D + L2D';
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