--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/tests/rDiff_poisson.m	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,96 @@
+function [P_VALUE, RET_STRUCT]= rDiff_poisson(CFG,gene,Counts_rDiff_parametric,Gene_expression)
+
+% Calculates the p-Values of a poisson test on each
+% alternative regions and combines the p-values using Bonferroni's correction
+
+
+%Initialize gene.name
+NR_OF_TRANS=size(gene.transcripts,2);
+if NR_OF_TRANS<=1
+    RET_STRUCT='NR_OF_TRANS too small';
+    P_VALUE=1;
+    return
+end
+
+
+%get the samples that are expressed (have more than 10 reads)
+TEMP_SAMPLE1=and(CFG.SAMPLES==1,Gene_expression>=10);
+TEMP_SAMPLE2=and(CFG.SAMPLES==2,Gene_expression>=10);
+SAMPLE1=find(TEMP_SAMPLE1);
+SAMPLE2=find(TEMP_SAMPLE2);
+
+%Check wether Counts_rDiff_parametric is nonempty
+for j=1:length(TEMP_SAMPLE1)
+  TEMP_SAMPLE1(j)=and(not(isempty(Counts_rDiff_parametric{j})), ...
+		      TEMP_SAMPLE1(j));
+end
+for j=1:length(TEMP_SAMPLE2)
+  TEMP_SAMPLE2(j)=and(not(isempty(Counts_rDiff_parametric{j})), ...
+		      TEMP_SAMPLE2(j));
+end
+
+SAMPLE1=find(TEMP_SAMPLE1);
+SAMPLE2=find(TEMP_SAMPLE2);
+
+
+
+SAMPLE_LENGTH1=length(SAMPLE1);
+SAMPLE_LENGTH2=length(SAMPLE2);
+
+if min(SAMPLE_LENGTH1,SAMPLE_LENGTH2)==0
+    RET_STRUCT='SAMPLE_LENGTH too small';
+    P_VALUE=1;
+    return
+end
+ 
+% Get the region counts
+region_counts_1=zeros(SAMPLE_LENGTH1,length(Counts_rDiff_parametric{1,1}));
+for j=1:SAMPLE_LENGTH1
+    region_counts_1(j,:)=Counts_rDiff_parametric{1,SAMPLE1(j)};
+end
+region_counts_2=zeros(SAMPLE_LENGTH2,length(Counts_rDiff_parametric{1,1}));
+for j=1:SAMPLE_LENGTH2
+    region_counts_2(j,:)=Counts_rDiff_parametric{1,SAMPLE2(j)};
+end
+
+% Get the gene expression
+gene_expression_1=sum(Gene_expression(SAMPLE1));
+gene_expression_2=sum(Gene_expression(SAMPLE2));
+
+%compute the p-values
+OBSERVED_COUNTS=[sum(region_counts_1,1);sum(region_counts_2,1)];
+TOTAL_COUNTS=sum(OBSERVED_COUNTS,1);
+
+%calculate gene expression ratio
+LAMBDA=gene_expression_1/(gene_expression_2+gene_expression_1);
+
+
+P_LIST=ones(1,size(TOTAL_COUNTS,2));
+%Iterate over the regions
+SKIPPED_TESTS=0;
+for i=1:length(P_LIST)
+    if sum(TOTAL_COUNTS(i))==0
+        SKIPPED_TESTS=SKIPPED_TESTS+1;
+        continue
+    end
+    
+    MEAN=LAMBDA*TOTAL_COUNTS(i);
+    VARIANCE=(TOTAL_COUNTS(i)*LAMBDA*(1-LAMBDA)).^0.5;      
+    Y=sum(((MEAN-OBSERVED_COUNTS(1,i))./VARIANCE).^2).^0.5;
+    
+    %Calculate the p-value
+    P_VALUE=1-gammainc((Y^2)/2,1/2);
+    
+    P_LIST(i)=P_VALUE;
+end
+if length(P_LIST)-SKIPPED_TESTS<=0
+  P_VALUE=1;
+else
+  P_VALUE=min(P_LIST)*(length(P_LIST)-SKIPPED_TESTS);
+end
+
+RET_STRUCT={};
+return
+
+
+