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ImmunoScore_IFM1_calculation.m
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ImmunoScore_IFM1_calculation.m
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%% Calculate CD3+ & CD8+ in R1/R2 (for immunoscore)
tic;
for s=1:length(slideName)
disp(strcat('Processing:',slideName{s}));
data1 = eval(strcat('data',slideName{s}));
data1 = removevars(data1, 'TDist');
data1.CD3pR1 = data1.CD3ep & (data1.Region==1);
data1.CD3pR2 = data1.CD3ep & (data1.Region==2);
data1.CD8pR1 = data1.CD8ap & (data1.Region==1);
data1.CD8pR2 = data1.CD8ap & (data1.Region==2);
data1.R0 = data1.Region == 0;
data1.R1 = data1.Region == 1;
data1.R2 = data1.Region == 2;
eval(strcat('data',slideName{s},'=data1;'));
toc;
end
%% Generate immune scores;
sumAllsample.norm_CD8R1 = sumAllsample.mean_CD8pR1 ./sumAllsample.mean_R1;
sumAllsample.norm_CD8R2 = sumAllsample.mean_CD8pR2 ./sumAllsample.mean_R2;
sumAllsample.norm_CD3R1 = sumAllsample.mean_CD3pR1 ./sumAllsample.mean_R1;
sumAllsample.norm_CD3R2 = sumAllsample.mean_CD3pR2 ./sumAllsample.mean_R2;
Cutoff_CD3R1 = 0.03;
Cutoff_CD3R2 = 0.2;
Cutoff_CD8R1 = 0.025;
Cutoff_CD8R2 = 0.07;
sumAllsample.ImmunoScore = (sumAllsample.norm_CD3R1 > Cutoff_CD3R1) + (sumAllsample.norm_CD3R2 > Cutoff_CD3R2) + (sumAllsample.norm_CD8R1 > Cutoff_CD8R1) + (sumAllsample.norm_CD8R2 > Cutoff_CD8R2);