Skip to content
Permalink
master
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?

SciRep2020-Data-and-Files/HOV_Trial.m

Go to file
 
 
Cannot retrieve contributors at this time
348 lines (296 sloc) 17.5 KB
Raw Blame
Open in GitHub Desktop
% HOV_Trial.m
% HOV Trial Human ADI (Matei)
% Aug. 7, 2015 - Dec. 16, 2016
agarcomp = input('Compensate agar for HOV? (0/1)');
drug(1) = {'dmso'};
drug(2) = {'carb'};
drug(3) = {'tax+carb'};
drug(4) = {'tax'};
Ndrug = length(drug);
% patcoc.num = empty
% patcoc.class(1) = Binary Resist/Sens [1 5 6 9 11 14 16 17 18 19
% 20 22 23] [2 4 7 8 10 12 13 15 21]
% [21 2 10 19 8 12 4 6 3 7] [
pat(1) = {'hov5'}; patcoc(1) = 1; patreg(1) = {'CT'}; % S
pat(2) = {'hov7'}; patcoc(2) = -1; patreg(2) = {'clear'}; % S clear cell
pat(3) = {'hov8'}; patcoc(3) = -1; patreg(3) = {'CT'}; % R
pat(4) = {'hov8b'}; patcoc(4) = -1; patreg(4) = {'met'}; % met 8
pat(5) = {'hov9'}; patcoc(5) = 1; patreg(5) = {'met'}; % met
pat(6) = {'hov10'}; patcoc(6) = 1; patreg(6) = {'CT'}; % S
pat(7) = {'hov11'}; patcoc(7) = 1; patreg(7) = {'met'}; % met
pat(8) = {'hov12'}; patcoc(8) = 1; patreg(8) = {'met'}; % met
pat(9) = {'hov13'}; patcoc(9) = 1; patreg(9) = {'CT'}; % S
pat(10) = {'hov14'}; patcoc(10) = -1; patreg(10) = {'clear'}; % R
pat(11) = {'hov15'}; patcoc(11) = 1; patreg(11) = {'CT'}; % S
pat(12) = {'hov16'}; patcoc(12) = -1; patreg(12) = {'CT'}; % R
pat(13) = {'hov17'}; patcoc(13) = -1; patreg(13) = {'CT'}; % R
pat(14) = {'hov18a'}; patcoc(14) = 1; patreg(14) = {'CT'}; % S
pat(15) = {'hov18b'}; patcoc(15) = 1; patreg(15) = {'met'}; % met 18
pat(16) = {'hov20'}; patcoc(16) = 1; patreg(16) = {'CT'}; % S
pat(17) = {'hov20b'}; patcoc(17) = 1; patreg(17) = {'met'}; % met 20
pat(18) = {'hov22'}; patcoc(18) = 1; patreg(18) = {'CT'}; % S
pat(19) = {'hov23'}; patcoc(19) = 1; patreg(19) = {'CT'}; % S
pat(20) = {'hov25'}; patcoc(20) = 1; patreg(20) = {'CT'}; % S
pat(21) = {'hov26'}; patcoc(21) = 1; patreg(21) = {'met'}; % met
pat(22) = {'hov30'}; patcoc(22) = 1; patreg(22) = {'CT'}; % S
pat(23) = {'hov31'}; patcoc(23) = 1; patreg(23) = {'CT'}; % S
%pat(21) = {'hov27'}; patcoc(21) = -1;
%pat(24) = {'hov29'}; patcoc(24) = 0; % no cancer
%pat(25) = {'hov19'}; patcoc(25) = 0; % withdrawn
%pat(26) = {'hov21'}; patcoc(26) = 0; % withdrawn
%pat(27) = {'hov24'}; patcoc(27) = 0; % no platinum
%pat(28) = {'hov28'}; patcoc(28) = 0; % withdrawn
testvec = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23];
NpatTrial = length(pat);
% %%% Partial Outcome Set
% patind(2).num = [2 3 4 10 12 13]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [1 5 6 7 8 9 11]; patind(3).class = {'Sens'}; % sens
%%% Partial Outcome Set (flip hov9)
% patind(2).num = [2 3 4 10 12 13]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [1 6 7 8 9 11]; patind(3).class = {'Sens'}; % sens
% patind(4).num = 5; patind(4).class = {'Test'};
%%% Ordered Full Set
% patind(2).num = [2 13 14 16 19 24 25 10]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [3 4 5 6 7 8 23 12 1 9 11 17 18 20 21 22]; patind(3).class = {'Sens'}; % sens
%%% Self-ordered Clean Set
% patind(2).num = [2 10 12 13 14 15 16 18 19 24 25]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [3 4 5 6 7 8]; patind(3).class = {'Sens'}; % sens
% patind(4).num = [9 11 17 20 21 22 23]; patind(4).class = {'Test'};
%%% Full Set
% patind(2).num = [2 13 14 16 19 24 25]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [1 3 4 5 6 7 8 9 10 11 12 15 17 18 20 21 22 23]; patind(3).class = {'Sens'}; % sens
%%% First Set
% patind(2).num = [2 6]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [1 3 4 5 7 8]; patind(3).class = {'Sens'}; % sens
%%% Second Set
% patind(2).num = [13 14 16 19 24 25]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [9 10 11 12 15 17 18 20 21 22 23]; patind(3).class = {'Sens'}; % sens
%%% Immobilization set
% patind(2).num = [1 2 3 4 5 6 7 8]; patind(2).class = {'Resist'}; % resist [10 12 3 4 21 5 8 7]
% patind(3).num = [9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25]; patind(3).class = {'Sens'}; % sens
% Outcome based
% patind(2).num = [2 3 12 13]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [5 6 7 8 9]; patind(3).class = {'Sens'}; % sens
% patind(4).num = [17 20 25 4 11 14 15 16 23 24 10 18 21 22]; patind(4).class = {'Test'};
% 12/1/18 set
% patind(2).num = [2 3 4 10 12 13 24]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [1 5 6 7 8 9 11 14 15 17 19 20 23]; patind(3).class = {'Sens'}; % sens
% patind(2).num = [10 12 13 24]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [9 11 14 15 17 19 20 23]; patind(3).class = {'Sens'}; % sens
% patind(2).num = [2 3 4 10 12 13 5]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [1 6 7 8 9 11]; patind(3).class = {'Sens'}; % sens
% 12/5/18 Current best classification
% patind(2).num = [2 3 4 10 12 13 21]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [1 6 7 8 9 14 19 23]; patind(3).class = {'Sens'}; % sens
% % patind(4).num = [24 5 11 17 20]; patind(4).class = {'Test'}; % sens
% TClass = 0;
% PClass = 0;
% Held out: 1 12 14 15 17
% 12/5/18 Full set
% patind(2).num = [2 3 10 12 13 24 4]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [5 6 7 8 9 11 14 15 17 19 20 23]; patind(3).class = {'Sens'}; % sens
% Held out: 1
% 12/1/18 set for 3-class
% patind(2).num = [2 3 10 13 24]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [5 11 12 17 20]; patind(3).class = {'Mid'}; % sens
% patind(4).num = [4 6 7 8 9 14 19 23]; patind(4).class = {'Sens'}; % sens
% Outliers: 5 9
% % 9/16/19 Test Set
% patind(1).descrip = {'Test Set'};
% patind(2).num = [2 3 10 12 4 7 8 17]; patind(2).class = {'Class1'}; % resist
% patind(3).num = [15 5 21 9 11 14 16 18 19 20 22 23 24]; patind(3).class = {'Class2'}; % sens
% patind(4).num = [2 3 10 12 4 7 24]; patind(4).class = {'Test'}; % sens
% %patind(4).num = [2 3 10 12 4 7 8 17 15 5 21 9 11 14 16 18 19 20 22 23 1 6 13]; patind(4).class = {'Test'}; % sens
% VIS.PClass = 1; % Predict the third class
%
% 9/16/19 Full Set
% patind(1).descrip = {'Full Set'};
% patind(2).num = [2 3 4 10 12 13 21]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [1 5 6 7 8 9 11 14 15 16 17 18 19 20 22 23]; patind(3).class = {'Sens'}; % sens
% patind(4).num = [13 6 8]; patind(4).class = {'Test'}; % sens
% VIS.PClass = 1; % Predict the third class
% 9/16/19 Agar versus Poly-L
% patind(1).descrip = {'Agar vs Poly'};
% patind(2).num = [1 2 3 4 5 6 7 8]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [9 10 11 12 13 14 15 16 17 18 20 21 22 23]; patind(3).class = {'Sens'}; % sens
% patind(4).num = [1 9 19]; patind(4).class = {'Test'}; % sens
% VIS.PClass = 1; % Predict the third class
% 9/16/19 Poly Set
% patind(1).descrip = {'Poly Set'};
% patind(2).num = [10 12 13 21]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [19 20 15 16 9 11 14 17 18 22 23]; patind(3).class = {'Sens'}; % sens
% patind(4).num = [1 2 3 4 5 6 7 8]; patind(4).class = {'Test'}; % sens
% VIS.PClass = 1; % Predict the third class
% 9/28/19 Met Set
% patind(1).descrip = {'Met Set'};
% patind(2).num = [2 4 7 8 10 12 13 15 21]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [1 5 6 9 11 14 16 17 18 19 20 22 23]; patind(3).class = {'Sens'}; % sens
% patind(4).num = [13 6 8]; patind(4).class = {'Test'}; % sens
% VIS.PClass = 0; % Predict the third class
% 9/28/19 Clean Set
% patind(1).descrip = {'Clean Set'};
% patind(2).num = [3 4 5 2 12 10 11 15 18 20 21 23 9]; patind(2).class = {'Resist'}; % resist
% patind(3).num = [7 8 22 14 17]; patind(3).class = {'Sens'}; % sens
% patind(4).num = [13 1 6 7 8 16 19]; patind(4).class = {'Test'}; % sens
% VIS.PClass = 1; % Predict the third class
% % 2/12/20 Test Set for HOV paper
% patind(1).descrip = {'Test Set'};
% patind(2).num = [21 3 4 5 7 8]; patind(2).class = {'Class1'}; % resist
% patind(3).num = [1 2 15 17 23 9 14 18 11 20 16 19 22]; patind(3).class = {'Class2'}; % sens
% patind(4).num = [6 10 12 13]; patind(4).class = {'Test'}; % sens
% %patind(4).num = testvec; patind(4).class = {'Test'}; % sens
% VIS.PClass = 1; % Predict the third class
% % 2/13/20 Test Set
% patind(1).descrip = {'Test Set'};
% patind(2).num = [12 10 21]; patind(2).class = {'Class1'}; % resist
% patind(3).num = [15 24 23 9 14 18 11 19 20 16 22]; patind(3).class = {'Class2'}; % sens
% patind(4).num = [1 6 13]; patind(4).class = {'Test'}; % sens
% %patind(4).num = [2 3 10 12 4 7 8 17 15 5 21 9 11 14 16 18 19 20 22 23 1 6 13]; patind(4).class = {'Test'}; % sens
% VIS.PClass = 0; % Predict the third class
% Poly immob set 3/3/20
% patind(1).descrip = {'Test Set'};
% patind(2).num = [10 12 21 15 13]; patind(2).class = {'Class1'}; % resist
% patind(3).num = [17 23 9 14 18 19 11 20 16 22]; patind(3).class = {'Class2'}; % sens
% patind(4).num = [9 13 19]; patind(4).class = {'Test'}; % sens
% %patind(4).num = testvec; patind(4).class = {'Test'}; % sens
% VIS.PClass = 1; % Predict the third class
% % 4/22/20 Straight SciRep sequence
% patind(1).descrip = {'Test Set'};
% patind(2).num = [10 2 3 12 15 4 5 21 8 17 7]; patind(2).class = {'Class1'}; % resist
% patind(3).num = [1 14 19 18 22 9 23 11 16 20]; patind(3).class = {'Class2'}; % sens
% patind(4).num = [13 6]; patind(4).class = {'Test'}; patind(4).tcoc = [-1 1]; % -1 = Resist 1 = Sens
% %patind(4).num = testvec; patind(4).class = {'Test'};
% VIS.PClass = 1; % Predict the third class
% % 4/22/20 Poly
% patind(1).descrip = {'Test Set'};
% patind(2).num = [10 12 13]; patind(2).class = {'Class1'}; % resist
% patind(3).num = [14 19 18 22 9 23 11 16 20]; patind(3).class = {'Class2'}; % sens
% patind(4).num = [2 3 15 4 5 21 8 17 7 1 6]; patind(4).tcoc = zeros(1,11); patind(4).class = {'Test'};
% VIS.PClass = 1; % Predict the third class
% % 8/22/20 SciRep sequence
% patind(1).descrip = {'Test Set'};
% patind(2).num = [10 2 3 12 15 4 5 21 8 17 7]; patind(2).class = {'Class1'}; % resist
% patind(3).num = [1 14 19 18 22 9 23 11 16 20]; patind(3).class = {'Class2'}; % sens
% patind(4).num = [13 6]; patind(4).tcoc = [-1 1]; % -1 = Resist 1 = Sens
% %patind(4).num = testvec; patind(4).class = {'Test'};
% VIS.PClass = 1; % Predict the third class
% % AA 8/23/20 Train on Poly sorted by class
% patind(1).descrip = {'Test Set'};
% patind(2).num = [10 12 13]; patind(2).class = {'Class1'}; % resist
% patind(3).num = [9 11 14 16 18 19 20 22 23]; patind(3).class = {'Class2'}; % sens
% patind(4).num = [2 3 4 5 7 8 15 17 21 1 6]; patind(4).tcoc = zeros(1,11); patind(4).class = {'Test'};
% VIS.PClass = 1; % Predict the third class
% % BB 8/23/20 Train on Ag-Met-Pol sorted by class
% patind(1).descrip = {'Test Set'};
% patind(2).num = [2 3 10 12 4 5 7 8 15 17 21]; patind(2).class = {'Class1'}; % resist
% patind(3).num = [1 9 11 14 16 18 19 20 22 23]; patind(3).class = {'Class2'}; % sens
% patind(4).num = [13 6]; patind(4).class = {'Test'}; patind(4).tcoc = [-1 1]; % -1 = Resist 1 = Sens
% %patind(4).num = testvec; patind(4).class = {'Test'};
% VIS.PClass = 1; % Predict the third class
% % CC Ag-Pol matched to sortFV on AA
% patind(1).descrip = {'Test Set'};
% patind(2).num = [3 2 10 12 7 17 15 4 5 21 8]; patind(2).class = {'Class1'}; % resist
% patind(3).num = [11 23 9 16 20 1 14 19 18 22]; patind(3).class = {'Class2'}; % sens
% patind(4).num = [13 6]; patind(4).tcoc = zeros(1,2); patind(4).class = {'Test'};
% VIS.PClass = 1; % Predict the third class
% DD 8/23/20 Train on Agar-poly test mets matched to sortFV
patind(1).descrip = {'Test Set'};
patind(2).num = [2 3 10 12]; patind(2).class = {'Class1'}; % resist
patind(3).num = [1 9 11 14 16 18 19 20 22 23]; patind(3).class = {'Class2'}; % sens
patind(4).num = [4 5 7 8 15 17 21 13 6]; patind(4).class = {'Test'}; patind(4).tcoc = [0 0 0 0 0 0 0 -1 1]; % -1 = Resist 1 = Sens
%patind(4).num = testvec; patind(4).class = {'Test'};
VIS.PClass = 1; % Predict the third class
% % 8/27/20
% patind(1).descrip = {'Test Set'};
% patind(2).num = [3 13 2 10 12 7 17 15 4 5 21 8]; patind(2).class = {'Class1'}; % resist
% patind(3).num = [6 11 23 9 16 20 1 14 19 18 22]; patind(3).class = {'Class2'}; % sens
% patind(4).num = [13 6]; patind(4).tcoc = zeros(1,2); patind(4).class = {'Test'};
% VIS.PClass = 1; % Predict the third class
NpatRclass = length(patind(2).num);
NpatSclass = length(patind(3).num);
Ntest = 0;
Ntype = 3;
if VIS.PClass == 1
Ntest = length(patind(4).num);
Ntype = 4;
end
ind = 0;
for ploop = 1:NpatRclass
ind = ind + 1;
pctmp(ind) = -1;
end
for ploop = 1:NpatSclass
ind = ind + 1;
pctmp(ind) = +1;
end
PatClass = pctmp'; % Column vector with two-class labels
patind(1).num = concat(patind(2).num,patind(3).num);
patind(1).Npatc = length(patind(1).num);
patind(2).Npatc = length(patind(2).num);
patind(3).Npatc = length(patind(3).num);
Npat = length(patind(2).num) + length(patind(3).num); % Npat is only for 2-class ViewIntraSet uses
if VIS.PClass == 1
patind(4).Npatc = length(patind(4).num);
patind(5).num = concat(patind(1).num,patind(4).num);
patind(5).Npatc = length(patind(5).num);
Npatot = Npat + Ntest;
end
% patindtmp = [];
% for loop = 2:3
% patindtmp = concat(patindtmp,patind(loop).num);
% patind(loop).Npatc = length(patind(loop).num);
% end
% patind(1).num = patindtmp;
% patind(1).Npatc = length(patind(1).num);
for ploop = 1:Npat
patnm(ploop) = pat(patind(1).num(ploop));
end
if VIS.PClass == 1
VIS.Ntest = Ntest;
for ploop = 1:Ntest
patestnm(ploop) = pat(patind(4).num(ploop));
end
for ploop = 1:Npatot
patotnm(ploop) = pat(patind(5).num(ploop));
end
end
ind = 0; patex = 0;
np = length(testvec);
for loop = 1:np
if where(patind(1).num,testvec(loop)) == -1
ind = ind + 1;
patex(ind) = testvec(loop);
end
end
patex
% Missing data sets
pdmiss = zeros(NpatTrial,Ndrug);
load dbiHOV
Nsamp = length(dbi);
% Place classtype into dbi.growth
dbind = 0;
for sloop = 1:Nsamp
patname = dbi(sloop).cell;
flag = 0; ind = 0; patnum = 0;
while (flag == 0)&&(ind < NpatTrial)
ind = ind + 1;
if strcmp(char(pat(ind)),patname)
flag = 1;
patnum = ind;
end
end
if patnum > 0
dbind = dbind+1;
dbinew(dbind) = dbi(sloop);
for tloop = 2:3 % changed from Ntype 2/12/20
w = where(patind(tloop).num,patnum);
if w ~=-1
dbinew(dbind).growth = char(patind(tloop).class);
end
end
end
end
%keyboard
clearvars -GLOBAL dbi
global dbi
dbi = dbinew;