max/ourMELONS
1
0
Fork 0
Code Issues 1 Pull requests Projects Releases Packages Wiki Activity Actions

Added source Matlab code for reference

Browse source
This commit is contained in:
Waldir Leoncio 2019-12-16 16:47:21 +01:00
parent b8af977117
commit b5d99903d2
186 changed files with 61405 additions and 1 deletions
Download patch file Download diff file Expand all files Collapse all files

90
matlab/graph/allfreqsnew2.m Normal file
View file

@ -0,0 +1,90 @@
function [counts,noalle_est,prior,adjprior,rawalleles] = allfreqsnew2(rawdata, noalle_est)
% Filename: allfreqsnew2.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
noalle(i)=noalle(i)-1;
end
end
% Fomulate the raw data such that the value i in a entry denotes the ith
% alleles.
for i=1:dime(2)-1
rawalles=unique(rawdata(:,i));
% rawalles = [1:noalle(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);
rawdata(logical(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;
rawdata(logical(rawdata(:,i)==rawalles(j)),i)=ones(length(find(rawdata(:,i)==rawalles(j))),1)*j;
end
end
end
% ALLOWED_MEMORY = 50; % in unit of megabyte.
% n1 = max(noalle_est);
% n2 = dime(2)-1;
% n3 = double(max(rawdata(:,dime(2))));
% ncells = n1*n2*n3;
% memory_used = ncells/(1024*1024); % using uint8 format.
% if memory_used < ALLOWED_MEMORY
% counts=zeros(n1,n2,n3,'uint8');
% else
% nbatches = ceil(memory_used/ALLOWED_MEMORY);
% n3_in_batch = ceil(n3/nbatches);
% counts = cell(nbatches,1);
% for i=1:nbatches-1
% % counts = cat(3,counts,uint16(zeros(n1,n2,n3_in_batch)));
% counts{i} = zeros(n1,n2,n3_in_batch,'uint8');
% end
% % counts = cat(3, counts, uint16(zeros(n1,n2,n3-n3_in_batch*(nbatches-1))));
% counts{i} = zeros(n1,n2,n3-n3_in_batch*(nbatches-1),'uint8');
% end
counts = zeros(max(noalle_est),dime(2)-1,max(rawdata(:,dime(2))),'uint8');
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
maxnoalle = max(noalle_est);
% prior = [];
prior=zeros(maxnoalle,dime(2)-1);
for i=1:dime(2)-1
prior(:,i) = [SCALE*ones(noalle_est(i),1)/noalle_est(i);zeros(maxnoalle-noalle_est(i),1)];
end
adjprior=prior;
for i=1:dime(2)-1
adjprior(:,i)=adjprior(:,i)+[zeros(noalle_est(i),1);ones(maxnoalle-noalle_est(i),1)];
end