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1 function []=get_parametric_tests_caller(PAR)
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2
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3
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4 CFG = PAR.CFG;
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5 genes = PAR.genes;
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6 OUT_STR='';
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7
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8 % add paths
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9 addpath(CFG.paths);
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10 %load local variables
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11 data_dir=CFG.data_dir;
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12 OUT_STR=[];
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13
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14 variance_function_parametric_1=PAR.variance_function_parametric_1;
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15 variance_function_parametric_2=PAR.variance_function_parametric_2;
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16
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17 Counts_rDiff_parametric=PAR.Counts_rDiff_parametric;
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18 Gene_expression=PAR.Gene_expression;
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19
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20 %clear variabe PAR
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21 clear PAR;
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22
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23 NUMBER_OF_TESTS_PER_GENE=(CFG.perform_parametric+CFG.perform_poisson);
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24 if NUMBER_OF_TESTS_PER_GENE==0
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25 return
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26 end
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27 P_VALS=cell(size(genes,2),NUMBER_OF_TESTS_PER_GENE+12);
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28
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29
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30 %iterate over genes
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31 for i=1:size(genes,2)
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32 %TEMP_COUNT contains the counts for the current gene
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33 TEMP_COUNT=cell(1,3);
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34 gene = genes(i);
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35
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36
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37 OLD_OUT_STR=OUT_STR;
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38 OUT_STR=['Current gene: ' gene.name ' '];
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39 %print progress
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40 if CFG.use_rproc
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41 fprintf([OUT_STR '\n'])
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42 else
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43 % Erase old progress
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44 fprintf(repmat('\b',1,length(OLD_OUT_STR)));
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45 fprintf([OUT_STR])
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46 end
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47
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48 %set default return values
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49 P_VALS{i,1}=gene.name;
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50
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51 %check that the gene has exons defined
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52 if isempty(gene.exons)
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53 P_VALS{i,4}='Exons field empty in gene structure';
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54 continue;
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55 end
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56
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57 %check that the gene is longer than the Reads. Otherwise the
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58 %definition of regions does not makes sense
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59 if gene.stop-gene.start<CFG.sequenced_length+3
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60 P_VALS{i,4}='Gene to short';
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61 continue;
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62 end
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63 %perform
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64 COUNTER=2;
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65 if CFG.perform_parametric
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66 [PV, INFO]= rDiff_parametric(CFG,gene,Counts_rDiff_parametric(i,:),Gene_expression(i,:),variance_function_parametric_1, variance_function_parametric_2);
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67 P_VALS{i,COUNTER}={PV, INFO};
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68 COUNTER=COUNTER+1;
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69 end
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70
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71 if CFG.perform_poisson
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72 [PV, INFO]= rDiff_poisson(CFG,gene,Counts_rDiff_parametric(i,:),Gene_expression(i,:));
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73 P_VALS{i,COUNTER}={PV, INFO};
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74 end
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75
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76 end
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77
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78 fprintf('\n')
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79 %Save the p-values
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80 OUT_FILENAME=[CFG.outfile_prefix '.mat'];
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81 save(OUT_FILENAME,'P_VALS')
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82
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