-
Notifications
You must be signed in to change notification settings - Fork 0
/
kaplan_meier_and_mutation_analysis.m
47 lines (40 loc) · 2.08 KB
/
kaplan_meier_and_mutation_analysis.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
function kaplan_meier_and_mutation_analysis(filename_km, filename_mut, ...
outputDir, gene_name, numericData, patientsNames, ...
patientsNamesMutOtherDB, patientsNamesKM, geneNames, ...
geneNamesMut, timeData, cens, timeCutOff, print_config)
% Spliting patients according to whether they have a mutation ..
% in driver gene, or not.
[~, ~, patientsNamesMut, patientsNamesNotMut]...
= split_gene_data_by_patients_w_mutation(numericData, patientsNames, ...
patientsNamesMutOtherDB, gene_name, geneNamesMut);
% Kaplan Meier Analysis:
% Mutated 1st Gene (MG1), NotMutated 1st Gene (NMG1),
% High 2nd Gene expression (HG2), Low 2nd Gene expression (LG2)
% with the following combinations:
% MG1 + HG2, MG1 + LG2, NMG1 + HG2, NMG1 + LG2.
fileOutput = sprintf('KM_CandidateGenesVsMutated_%s_', gene_name);
KM_support_functions.kaplan_meier_gene1_vs_gene2_encapsulated(...
filename_km, fileOutput, outputDir, ...
gene_name, numericData, patientsNames, patientsNamesMut, ...
patientsNamesNotMut, patientsNamesKM,...
geneNames, timeData, cens, timeCutOff, 0.2, 0.8, 'mut_exp', ...
{filename_mut}, print_config);
KM_support_functions.kaplan_meier_gene1_vs_gene2_encapsulated(...
filename_km, fileOutput, outputDir, ...
gene_name, numericData, patientsNames, patientsNamesMut, ...
patientsNamesNotMut, patientsNamesKM,...
geneNames, timeData, cens, timeCutOff, 0.8, 0.2, 'mut_exp', ...
{filename_mut}, print_config);
KM_support_functions.kaplan_meier_gene1_vs_gene2_encapsulated(...
filename_km, fileOutput, outputDir, ...
gene_name, numericData, patientsNames, patientsNamesMut, ...
patientsNamesNotMut, patientsNamesKM,...
geneNames, timeData, cens, timeCutOff, 0.3, 0.7, 'mut_exp', ...
{filename_mut}, print_config);
KM_support_functions.kaplan_meier_gene1_vs_gene2_encapsulated(...
filename_km, fileOutput, outputDir, ...
gene_name, numericData, patientsNames, patientsNamesMut, ...
patientsNamesNotMut, patientsNamesKM,...
geneNames, timeData, cens, timeCutOff, 0.7, 0.3, 'mut_exp', ...
{filename_mut}, print_config);
end