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1 function [VARIANCE1, VARIANCE2]=estimate_variance_parametric(CFG,genes)
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2
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3 fprintf('Estimating variance function for rDiff.parametric\n')
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4
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5 VARIANCE1=[];
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6 VARIANCE2=[];
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7
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8 %Get the gene expression
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9 fprintf('Loading gene expression\n')
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10 if isempty(CFG.Counts_gene_expression)
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11 EXPR_TAB_FILENAME=[CFG.out_base 'Gene_expression.tab'];
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12 else
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13 EXPR_TAB_FILENAME=CFG.Counts_gene_expression;
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14 end
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15
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16 try
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17 Gene_expression=importdata(EXPR_TAB_FILENAME,'\t',1);
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18 catch
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19 error(['Could not open: ' EXPR_TAB_FILENAME])
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20 end
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21 %C=importdata('../out/release_test/Gene_expression.tab','\t',1);
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22
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23
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24 %Get the counts
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25 fprintf('Loading alternative region counts\n')
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26 if isempty(CFG.Counts_rDiff_parametric)
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27 IN_FILENAME=[CFG.out_base 'Alternative_region_counts.mat'];
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28 load(IN_FILENAME,'Counts_rDiff_parametric')
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29 else
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30 IN_FILENAME=[CFG.out_base CFG.Counts_rDiff_parametric];
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31 load(IN_FILENAMEc,'Counts_rDiff_parametric')
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32 end
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33
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34 %Iterate over the functions to be generated
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35 %compute means and variances
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36
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37 if CFG.compute_variance_function_1
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38 fprintf('estimating variance function for sample 1\n')
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39 %Get the samples to use for the for estimation the variance function
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40 if CFG.merge_sample1
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41 SAMPLE_IX=find(CFG.SAMPLES);
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42 else
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43 SAMPLE_IX=find(CFG.SAMPLES==1);
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44 end
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45 VARIANCE1=estimate_variance_helper(CFG,SAMPLE_IX,Counts_rDiff_parametric,Gene_expression.data);
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46 if not(isempty(CFG.save_variance_function_1))
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47 VARIANCE_FUNTION_OUTPATH=[CFG.out_base CFG.save_variance_function_1];
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48 save(VARIANCE_FUNTION_OUTPATH,'VARIANCE1');
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49 else
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50 %Use previously estimated variance function
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51 if not(isempty(CFG.variance_function_1))
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52 try
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53 VARIANCE_FUNTION_INPATH=[CFG.out_base CFG.variance_function_1];
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54 VARIANCE1=load(VARIANCE_FUNTION_INPATH);
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55 catch
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56 error(['Could not load variance function for sample 1 from: ' VARIANCE_FUNTION_INPATH])
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57 end
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58 end
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59 end
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60 end
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61
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62 if CFG.compute_variance_function_2
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63 fprintf('estimating variance function for sample 2\n')
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64 %Get the samples to use for the for estimation the variance function
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65 if CFG.merge_sample2
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66 SAMPLE_IX=find(CFG.SAMPLES);
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67 else
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68 SAMPLE_IX=find(CFG.SAMPLES==2);
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69 end
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70 VARIANCE2=estimate_variance_helper(CFG,SAMPLE_IX,Counts_rDiff_parametric,Gene_expression.data);
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71 if not(isempty(CFG.save_variance_function_2))
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72 VARIANCE_FUNTION_OUTPATH=[CFG.out_base CFG.save_variance_function_2];
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73 save(VARIANCE_FUNTION_OUTPATH,'VARIANCE2');
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74 else
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75 %Use previously estimated variance function
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76 if not(isempty(CFG.variance_function_2))
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77 try
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78 VARIANCE_FUNTION_INPATH=[CFG.out_base CFG.variance_function_2];
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79 VARIANCE2=load(VARIANCE_FUNTION_INPATH);
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80 catch
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81 error(['Could not load variance function for sample 2 from: ' VARIANCE_FUNTION_INPATH])
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82 end
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83 end
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84 end
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85 end
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86
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87
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88
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