Added source Matlab code for reference

matlab/linkage/allfreqsnew3.m

@@ -0,0 +1,63 @@
+function [counts,noalle,prior,adjprior,rawalleles,rawdata] = allfreqsnew(rawdata)
+% Filename: allfreqsnew.m
+% [counts,noalle,prior,adjprior,rawalleles] = allfreqsnew(rawdata)
+%
+% Description:
+% rawdata has n rows (2 x #individuals) and n(l) first
+% colums are the loci. The last column is the subpopindex
+% prior is a created matrix of positive Dirichlet hyperparameters
+% missing data is filtered out
+% !!!NEW!!!zeros are accepted as allele codes and any negative numbers as missing data.
+
+% Modified by: Jing Tang
+
+SCALE = 1;
+dime=size(rawdata);
+noalle=zeros(dime(2)-1,1);
+rawalleles=cell(1,dime(2)-1);
+for i=1:dime(2)-1
+   noalle(i)=length(unique(rawdata(:,i)));
+end
+for i=1:dime(2)-1
+   if length(find(rawdata(:,i)<=0))>0 % filtering out the missing data
+      noalle(i)=noalle(i)-1;
+   end
+end
+for i=1:dime(2)-1
+    rawalles=unique(rawdata(:,i));
+    if rawalles(1)<=0
+        rawalles(1)=-999;
+    end
+    rawalleles{i} = rawalles;    % rawalleles!!!
+    if rawalles(1)<=0
+    for j=2:noalle(i)+1
+        rawdata(find(rawdata(:,i)==rawalles(j)),i)=ones(length(find(rawdata(:,i)==rawalles(j))),1)*(j-1);
+    end
+    else
+    for j=1:noalle(i)
+        rawdata(find(rawdata(:,i)==rawalles(j)),i)=ones(length(find(rawdata(:,i)==rawalles(j))),1)*j;
+    end
+end
+end
+
+        
+counts=zeros(max(noalle),dime(2)-1,max(rawdata(:,dime(2))));
+
+for i=1:dime(1)
+   for j=1:dime(2)-1
+      if rawdata(i,j)>0
+         counts(rawdata(i,j),j,rawdata(i,dime(2)))=...
+            counts(rawdata(i,j),j,rawdata(i,dime(2)))+1;
+      end
+   end
+end
+
+prior=[];
+for i=1:dime(2)-1
+   prior=[prior [SCALE*ones(noalle(i),1)/noalle(i);zeros(max(noalle)-noalle(i),1)]];
+end
+
+adjprior=prior;
+for i=1:dime(2)-1
+   adjprior(:,i)=adjprior(:,i)+[zeros(noalle(i),1);ones(max(noalle)-noalle(i),1)];
+end