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1 function []=rdiff(ARGS)
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2 % rdiff()
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3 %
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4
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5 if isempty(ARGS)
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6 usage() ;
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7 exit(-1) ;
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8 end
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9 %ARGS=[ARGS ':.:.'] ;
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10
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11 %%% Add paths %%%
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12 fprintf('Set the paths\n')
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13 CFG.paths = set_rdiff_paths();
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14
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15
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16 %%% Read configuration file %%%
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17 fprintf('Load configuration\n')
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18 CFG = configure_rdiff(CFG);
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19 CFG = process_command_line_args(CFG,ARGS);
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20 CFG = process_configure_rdiff(CFG);
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21
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22 %%% Get read counts %%%
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23
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24 %load the gene structure
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25 load(CFG.genes_path , 'genes');
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26
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27 % mask the regions which overlap with other genes
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28 fprintf('Compute regions common to multiple genes\n')
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29 [genes]=detect_overlapping_regions(genes);
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30
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31 %Precompute testing regions
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32 fprintf('Compute alternative regions\n')
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33 [genes]=compute_testing_region(CFG,genes);
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34
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35 %Get the gene expression
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36 if CFG.estimate_gene_expression
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37 fprintf('Measure gene expression\n')
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38 get_read_counts(CFG,genes);
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39 end
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40
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41 %%% Estimate variance function %%%
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42 if CFG.perform_nonparametric
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43 variance_function_nonparametric_1=[];
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44 variance_function_nonparametric_2=[];
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45 [variance_function_nonparametric_1, variance_function_nonparametric_2]=estimate_variance_nonparametric(CFG,genes);
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46 end
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47
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48 if CFG.perform_poisson
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49 variance_function_parametric_1=[];
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50 variance_function_parametric_2=[];
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51 end
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52 if CFG.perform_parametric
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53 variance_function_parametric_1=[];
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54 variance_function_parametric_2=[];
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55 [variance_function_parametric_1, variance_function_parametric_2]=estimate_variance_parametric(CFG,genes);
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56 end
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57
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58 %If only gene expression is needed, stop here
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59 if CFG.only_gene_expression
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60 return
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61 end
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62
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63
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64 %%% Perform tests & Write output %%%
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65
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66 %Run the prametric tests
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67 if or(CFG.perform_parametric,CFG.perform_poisson)
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68 perform_parametric_tests(CFG,genes,variance_function_parametric_1, variance_function_parametric_2)
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69 end
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70 %Run the nonparametric tests
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71 if or(CFG.perform_nonparametric,CFG.perform_mmd)
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72 perform_nonparametric_tests(CFG,genes,variance_function_nonparametric_1, variance_function_nonparametric_2)
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73 end
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74
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75 return
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76
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77
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78
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