diff rDiff/src/get_parametric_tests_caller.m @ 0:0f80a5141704

version 0.3 uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/get_parametric_tests_caller.m	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,82 @@
+function []=get_parametric_tests_caller(PAR)
+
+
+CFG = PAR.CFG;
+genes = PAR.genes;
+OUT_STR='';
+
+% add paths
+addpath(CFG.paths);
+%load local variables
+data_dir=CFG.data_dir;
+OUT_STR=[];
+
+variance_function_parametric_1=PAR.variance_function_parametric_1;
+variance_function_parametric_2=PAR.variance_function_parametric_2;
+
+Counts_rDiff_parametric=PAR.Counts_rDiff_parametric;
+Gene_expression=PAR.Gene_expression;
+
+%clear variabe PAR
+clear PAR;
+
+NUMBER_OF_TESTS_PER_GENE=(CFG.perform_parametric+CFG.perform_poisson);
+if NUMBER_OF_TESTS_PER_GENE==0
+    return
+end
+P_VALS=cell(size(genes,2),NUMBER_OF_TESTS_PER_GENE+12);
+
+
+%iterate over genes
+for i=1:size(genes,2)
+  %TEMP_COUNT contains the counts for the current gene
+  TEMP_COUNT=cell(1,3);
+  gene = genes(i);
+  
+  
+  OLD_OUT_STR=OUT_STR;
+  OUT_STR=['Current gene: ' gene.name ' '];
+  %print progress
+  if CFG.use_rproc
+      fprintf([OUT_STR '\n'])
+  else
+      % Erase old progress
+      fprintf(repmat('\b',1,length(OLD_OUT_STR)));
+      fprintf([OUT_STR])
+  end
+  
+  %set default return values
+  P_VALS{i,1}=gene.name;
+  
+  %check that the gene has exons defined
+  if isempty(gene.exons)
+    P_VALS{i,4}='Exons field empty in gene structure';
+    continue;
+  end
+
+  %check that the gene is longer than the Reads. Otherwise the
+  %definition of regions does not makes sense
+  if gene.stop-gene.start<CFG.sequenced_length+3
+    P_VALS{i,4}='Gene to short';
+    continue;
+  end
+  %perform 
+  COUNTER=2;
+  if CFG.perform_parametric
+      [PV, INFO]= rDiff_parametric(CFG,gene,Counts_rDiff_parametric(i,:),Gene_expression(i,:),variance_function_parametric_1, variance_function_parametric_2);
+      P_VALS{i,COUNTER}={PV, INFO};
+      COUNTER=COUNTER+1;
+  end
+      
+  if CFG.perform_poisson
+      [PV, INFO]= rDiff_poisson(CFG,gene,Counts_rDiff_parametric(i,:),Gene_expression(i,:));
+      P_VALS{i,COUNTER}={PV, INFO};
+  end
+  
+end
+
+fprintf('\n')
+%Save the p-values
+OUT_FILENAME=[CFG.outfile_prefix '.mat'];
+save(OUT_FILENAME,'P_VALS')
+