--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/tests/rDiff_mmd.m	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,48 @@
+function [pval,info] = rDiff_mmd(CFG,reads1,reads2)
+% simple application of mmd to test for differential distributions
+% of reads1, reads2
+% reads1: N1 x L
+% reads2: N2 x L
+
+
+bootstraps=CFG.bootstraps;
+
+
+% ensure reads are sparse and remove zero collumns
+%reads1temp = sparse(reads1(:,sum([reads1;reads2],1)>0));
+%reads2 = sparse(reads2(:,sum([reads1;reads2],1)>0));
+%reads1=reads1temp;
+
+statistic = eucl_dist(mean(reads1,1),mean(reads2,1))^2;
+
+allreads = [reads1;reads2];
+
+N1 = size(reads1,1);
+N2 = size(reads2,1);
+N = N1 + N2;
+
+ 
+%Use the transpose to make the selection of columms faster
+all_reads_trans=allreads';
+
+%bootstraping
+for i = 1:bootstraps
+
+  r = randperm(N);
+  
+  sample1 = all_reads_trans(:,r(1:N1));
+  sample2 = all_reads_trans(:,r(N1+1:N));
+  
+  bootstrap_results(i) = eucl_dist(mean(sample1,2), mean(sample2,2))^2;
+   
+end
+
+%Calculate the p-value
+pval =  min(1,double(1+sum(bootstrap_results >= statistic)) / bootstraps);
+info = [];
+
+
+
+function result = eucl_dist(A,B)
+
+result = sqrt(sum( (A - B) .^ 2 ));