90 lines
3 KiB
Matlab
90 lines
3 KiB
Matlab
function [counts,noalle_est,prior,adjprior,rawalleles] = allfreqsnew2(rawdata, noalle_est)
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% Filename: allfreqsnew2.m
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% [counts,noalle,prior,adjprior,rawalleles] = allfreqsnew(rawdata)
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%
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% Description:
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% rawdata has n rows (2 x #individuals) and n(l) first
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% colums are the loci. The last column is the subpopindex
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% prior is a created matrix of positive Dirichlet hyperparameters
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% missing data is filtered out
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% !!!NEW!!!zeros are accepted as allele codes and any negative numbers as missing data.
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% Modified by: Jing Tang
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SCALE = 1;
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dime=size(rawdata);
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noalle=zeros(dime(2)-1,1);
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rawalleles=cell(1,dime(2)-1);
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for i=1:dime(2)-1
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noalle(i)=length(unique(rawdata(:,i)));
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end
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for i=1:dime(2)-1
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if length(find(rawdata(:,i)<=0))>0
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noalle(i)=noalle(i)-1;
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end
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end
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% Fomulate the raw data such that the value i in a entry denotes the ith
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% alleles.
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for i=1:dime(2)-1
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rawalles=unique(rawdata(:,i));
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% rawalles = [1:noalle(i)]';
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if rawalles(1)<=0
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rawalles(1)=-999;
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end
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rawalleles{i} = rawalles; %rawalleles!!!
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if rawalles(1)<0
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for j=2:noalle(i)+1
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%rawdata(find(rawdata(:,i)==rawalles(j)),i)=ones(length(find(rawdata(:,i)==rawalles(j))),1)*(j-1);
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rawdata(logical(rawdata(:,i)==rawalles(j)),i)=ones(length(find(rawdata(:,i)==rawalles(j))),1)*(j-1);
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end
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else
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for j=1:noalle(i)
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% rawdata(find(rawdata(:,i)==rawalles(j)),i)=ones(length(find(rawdata(:,i)==rawalles(j))),1)*j;
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rawdata(logical(rawdata(:,i)==rawalles(j)),i)=ones(length(find(rawdata(:,i)==rawalles(j))),1)*j;
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end
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end
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end
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% ALLOWED_MEMORY = 50; % in unit of megabyte.
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% n1 = max(noalle_est);
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% n2 = dime(2)-1;
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% n3 = double(max(rawdata(:,dime(2))));
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% ncells = n1*n2*n3;
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% memory_used = ncells/(1024*1024); % using uint8 format.
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% if memory_used < ALLOWED_MEMORY
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% counts=zeros(n1,n2,n3,'uint8');
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% else
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% nbatches = ceil(memory_used/ALLOWED_MEMORY);
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% n3_in_batch = ceil(n3/nbatches);
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% counts = cell(nbatches,1);
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% for i=1:nbatches-1
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% % counts = cat(3,counts,uint16(zeros(n1,n2,n3_in_batch)));
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% counts{i} = zeros(n1,n2,n3_in_batch,'uint8');
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% end
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% % counts = cat(3, counts, uint16(zeros(n1,n2,n3-n3_in_batch*(nbatches-1))));
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% counts{i} = zeros(n1,n2,n3-n3_in_batch*(nbatches-1),'uint8');
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% end
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counts = zeros(max(noalle_est),dime(2)-1,max(rawdata(:,dime(2))),'uint8');
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for i=1:dime(1)
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for j=1:dime(2)-1
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if rawdata(i,j)>0
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counts(rawdata(i,j),j,rawdata(i,dime(2)))=...
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counts(rawdata(i,j),j,rawdata(i,dime(2)))+1;
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end
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end
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end
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maxnoalle = max(noalle_est);
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% prior = [];
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prior=zeros(maxnoalle,dime(2)-1);
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for i=1:dime(2)-1
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prior(:,i) = [SCALE*ones(noalle_est(i),1)/noalle_est(i);zeros(maxnoalle-noalle_est(i),1)];
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end
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adjprior=prior;
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for i=1:dime(2)-1
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adjprior(:,i)=adjprior(:,i)+[zeros(noalle_est(i),1);ones(maxnoalle-noalle_est(i),1)];
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end
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