Added source Matlab code for reference
This commit is contained in:
Waldir Leoncio
parent
b8af977117
commit
b5d99903d2
186 changed files with 61405 additions and 1 deletions
622
matlab/admixture/admix2.m
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622
matlab/admixture/admix2.m
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function admix2
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global PARTITION; global COUNTS;
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global SUMCOUNTS;
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clearGlobalVars;
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input_type = questdlg('Specify the format of your data: ',...
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'Specify Data Format', ...
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'BAPS-format', 'GenePop-format', 'BAPS-format');
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switch input_type
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case 'BAPS-format'
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waitALittle;
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[filename, pathname] = uigetfile('*.txt', 'Load data in BAPS-format');
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if filename==0
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return;
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end
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data = load([pathname filename]);
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ninds = testaaOnkoKunnollinenBapsData(data); %TESTAUS
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if (ninds==0)
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disp('Incorrect Data-file.');
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return;
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end
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h0 = findobj('Tag','filename1_text');
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set(h0,'String',filename); clear h0;
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waitALittle;
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[filename, pathname] = uigetfile('*.txt', 'Load Partition');
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if filename==0
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return;
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end
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PARTITION = load([pathname filename]);
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if ~(size(PARTITION,2)==1) | ~(size(PARTITION,1)==ninds)
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disp('Incorrect Partition-file.');
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return;
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end
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input_pops = questdlg(['When using data which are in BAPS-format, '...
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'you can specify the sampling populations of the individuals by '...
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'giving two additional files: one containing the names of the '...
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'populations, the other containing the indices of the first '...
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'individuals of the populations. Do you wish to specify the '...
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'sampling populations?'], ...
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'Specify sampling populations?',...
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'Yes', 'No', 'No');
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if isequal(input_pops,'Yes')
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waitALittle;
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[namefile, namepath] = uigetfile('*.txt', 'Load population names');
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if namefile==0
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kysyToinen = 0;
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else
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kysyToinen = 1;
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end
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if kysyToinen==1
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waitALittle;
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[indicesfile, indicespath] = uigetfile('*.txt', 'Load population indices');
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if indicesfile==0
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popnames = [];
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else
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popnames = initPopNames([namepath namefile],[indicespath indicesfile]);
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end
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else
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popnames = [];
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end
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else
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popnames = [];
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end
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[data, rowsFromInd, alleleCodes, noalle, adjprior, priorTerm] = handleData(data);
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data = data(:, 1:end-1);
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npops = length(unique(PARTITION(find(PARTITION>=0))));
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case 'GenePop-format'
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waitALittle;
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[filename, pathname] = uigetfile('*.txt', 'Load data in GenePop-format');
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if filename==0
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return;
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end
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kunnossa = testaaGenePopData([pathname filename]);
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if kunnossa==0
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return
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end
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[data,popnames]=lueGenePopData([pathname filename]);
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h0 = findobj('Tag','filename1_text');
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set(h0,'String',filename); clear h0;
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[data, rowsFromInd, alleleCodes, noalle, adjprior, priorTerm] = handleData(data);
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data = data(:, 1:end-1);
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npops = size(popnames,1);
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ninds = size(data,1)/rowsFromInd;
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PARTITION = zeros(ninds,1);
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ind = 1;
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for pop = 1:npops-1
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while (ind < popnames{pop+1,2})
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PARTITION(ind) = pop;
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ind = ind+1;
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end
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end
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while (ind <= ninds)
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PARTITION(ind) = npops;
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ind = ind+1;
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end
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all_in_text = questdlg(['Do you wish to use also the last population in the ',...
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'data to define one more population for admixture analysis: '],...
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'Define a population based on the last population in the data?', ...
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'Yes', 'No', 'Yes');
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if isequal(all_in_text, 'No')
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PARTITION(find(PARTITION==npops)) = -1;
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npops = npops-1;
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end
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otherwise return
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end
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initialPartition = PARTITION(:,ones(1,rowsFromInd))';
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initialPartition = initialPartition(:);
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[sumcounts, counts, logml] = ...
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initialCounts(initialPartition, data, npops, rowsFromInd, noalle);
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COUNTS = counts; SUMCOUNTS = sumcounts;
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clear('initialPartition', 'counts', 'sumcounts', ...
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'filename', 'ind', 'input_type', ...
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'logml', 'ninds', 'pathname', 'pop', 'priorTerm');
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clear('indicesfile','indicespath','input_pops','kysyToinen',...
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'namefile','namepath');
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c.PARTITION = PARTITION; c.COUNTS = COUNTS; c.SUMCOUNTS = SUMCOUNTS;
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c.alleleCodes = alleleCodes; c.adjprior = adjprior; c.popnames = popnames;
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c.rowsFromInd = rowsFromInd; c.data = data; c.npops = npops; c.noalle = noalle;
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admix1(c);
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%------------------------------------------------------------------------
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function clearGlobalVars
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global COUNTS; COUNTS = [];
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global SUMCOUNTS; SUMCOUNTS = [];
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global PARTITION; PARTITION = [];
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global POP_LOGML; POP_LOGML = [];
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%--------------------------------------------------------
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function ninds = testaaOnkoKunnollinenBapsData(data)
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%Tarkastaa onko viimeisessä sarakkeessa kaikki
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%luvut 1,2,...,n johonkin n:ään asti.
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%Tarkastaa lisäksi, että on vähintään 2 saraketta.
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if size(data,1)<2
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ninds = 0; return;
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end
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lastCol = data(:,end);
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ninds = max(lastCol);
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if ~isequal((1:ninds)',unique(lastCol))
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ninds = 0; return;
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end
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%-----------------------------------------------------------------------------------
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function popnames = initPopNames(nameFile, indexFile)
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%Palauttaa tyhjän, mikäli nimitiedosto ja indeksitiedosto
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% eivät olleet yhtä pitkiä.
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popnames = [];
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indices = load(indexFile);
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fid = fopen(nameFile);
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if fid == -1
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%File didn't exist
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msgbox('Loading of the population names was unsuccessful', ...
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'Error', 'error');
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return;
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end;
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line = fgetl(fid);
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counter = 1;
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while (line ~= -1) & ~isempty(line)
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names{counter} = line;
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line = fgetl(fid);
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counter = counter + 1;
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end;
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fclose(fid);
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if length(names) ~= length(indices)
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disp('The number of population names must be equal to the number of ');
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disp('entries in the file specifying indices of the first individuals of ');
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disp('each population.');
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return;
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end
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popnames = cell(length(names), 2);
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for i = 1:length(names)
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popnames{i,1} = names(i);
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popnames{i,2} = indices(i);
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end
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%---------------------------------------------------------------------------------------
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function [newData, rowsFromInd, alleleCodes, noalle, adjprior, priorTerm] = ...
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handleData(raw_data)
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% Alkuperäisen datan viimeinen sarake kertoo, miltä yksilöltä
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% kyseinen rivi on peräisin. Funktio tutkii ensin, että montako
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% riviä maksimissaan on peräisin yhdeltä yksilöltä, jolloin saadaan
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% tietää onko kyseessä haploidi, diploidi jne... Tämän jälkeen funktio
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% lisää tyhjiä rivejä niille yksilöille, joilta on peräisin vähemmän
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% rivejä kuin maksimimäärä.
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% Mikäli jonkin alleelin koodi on =0, funktio muuttaa tämän alleelin
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% koodi pienimmäksi koodiksi, joka isompi kuin mikään käytössä oleva koodi.
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% Tämän jälkeen funktio muuttaa alleelikoodit siten, että yhden lokuksen j
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% koodit saavat arvoja välillä 1,...,noalle(j).
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data = raw_data;
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nloci=size(raw_data,2)-1;
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dataApu = data(:,1:nloci);
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nollat = find(dataApu==0);
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if ~isempty(nollat)
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isoinAlleeli = max(max(dataApu));
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dataApu(nollat) = isoinAlleeli+1;
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data(:,1:nloci) = dataApu;
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end
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dataApu = []; nollat = []; isoinAlleeli = [];
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noalle=zeros(1,nloci);
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alleelitLokuksessa = cell(nloci,1);
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for i=1:nloci
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alleelitLokuksessaI = unique(data(:,i));
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alleelitLokuksessa{i,1} = alleelitLokuksessaI(find(alleelitLokuksessaI>=0));
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noalle(i) = length(alleelitLokuksessa{i,1});
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end
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alleleCodes = zeros(max(noalle),nloci);
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for i=1:nloci
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alleelitLokuksessaI = alleelitLokuksessa{i,1};
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puuttuvia = max(noalle)-length(alleelitLokuksessaI);
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alleleCodes(:,i) = [alleelitLokuksessaI; zeros(puuttuvia,1)];
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end
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for loc = 1:nloci
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for all = 1:noalle(loc)
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data(find(data(:,loc)==alleleCodes(all,loc)), loc)=all;
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end;
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end;
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nind = max(data(:,end));
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nrows = size(data,1);
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ncols = size(data,2);
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rowsFromInd = zeros(nind,1);
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for i=1:nind
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rowsFromInd(i) = length(find(data(:,end)==i));
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end
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maxRowsFromInd = max(rowsFromInd);
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a = -999;
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emptyRow = repmat(a, 1, ncols);
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lessThanMax = find(rowsFromInd < maxRowsFromInd);
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missingRows = maxRowsFromInd*nind - nrows;
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data = [data; zeros(missingRows, ncols)];
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pointer = 1;
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for ind=lessThanMax' %Käy läpi ne yksilöt, joilta puuttuu rivejä
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miss = maxRowsFromInd-rowsFromInd(ind); % Tältä yksilöltä puuttuvien lkm.
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for j=1:miss
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rowToBeAdded = emptyRow;
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rowToBeAdded(end) = ind;
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data(nrows+pointer, :) = rowToBeAdded;
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pointer = pointer+1;
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end
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end
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data = sortrows(data, ncols); % Sorttaa yksilöiden mukaisesti
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newData = data;
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rowsFromInd = maxRowsFromInd;
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adjprior = zeros(max(noalle),nloci);
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priorTerm = 0;
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for j=1:nloci
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adjprior(:,j) = [repmat(1/noalle(j), [noalle(j),1]) ; ones(max(noalle)-noalle(j),1)];
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priorTerm = priorTerm + noalle(j)*gammaln(1/noalle(j));
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end
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%--------------------------------------------------------------------
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function kunnossa = testaaGenePopData(tiedostonNimi)
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% kunnossa == 0, jos data ei ole kelvollinen genePop data.
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% Muussa tapauksessa kunnossa == 1.
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kunnossa = 0;
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fid = fopen(tiedostonNimi);
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line1 = fgetl(fid); %ensimmäinen rivi
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line2 = fgetl(fid); %toinen rivi
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line3 = fgetl(fid); %kolmas
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if (isequal(line1,-1) | isequal(line2,-1) | isequal(line3,-1))
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disp('Incorrect file format 1168'); fclose(fid);
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return
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end
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if (testaaPop(line1)==1 | testaaPop(line2)==1)
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disp('Incorrect file format 1172'); fclose(fid);
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return
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end
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if testaaPop(line3)==1
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%2 rivi tällöin lokusrivi
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nloci = rivinSisaltamienMjonojenLkm(line2);
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line4 = fgetl(fid);
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if isequal(line4,-1)
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disp('Incorrect file format 1180'); fclose(fid);
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return
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end
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if ~any(line4==',')
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% Rivin neljä täytyy sisältää pilkku.
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disp('Incorrect file format 1185'); fclose(fid);
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return
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end
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pointer = 1;
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while ~isequal(line4(pointer),',') %Tiedetään, että pysähtyy
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pointer = pointer+1;
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end
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line4 = line4(pointer+1:end); %pilkun jälkeinen osa
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nloci2 = rivinSisaltamienMjonojenLkm(line4);
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if (nloci2~=nloci)
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disp('Incorrect file format 1195'); fclose(fid);
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return
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end
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else
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line = fgetl(fid);
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lineNumb = 4;
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while (testaaPop(line)~=1 & ~isequal(line,-1))
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line = fgetl(fid);
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lineNumb = lineNumb+1;
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end
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if isequal(line,-1)
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disp('Incorrect file format 1206'); fclose(fid);
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return
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end
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nloci = lineNumb-2;
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line4 = fgetl(fid); %Eka rivi pop sanan jälkeen
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if isequal(line4,-1)
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disp('Incorrect file format 1212'); fclose(fid);
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return
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end
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if ~any(line4==',')
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% Rivin täytyy sisältää pilkku.
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disp('Incorrect file format 1217'); fclose(fid);
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return
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end
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pointer = 1;
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while ~isequal(line4(pointer),',') %Tiedetään, että pysähtyy.
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pointer = pointer+1;
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end
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line4 = line4(pointer+1:end); %pilkun jälkeinen osa
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nloci2 = rivinSisaltamienMjonojenLkm(line4);
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if (nloci2~=nloci)
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disp('Incorrect file format 1228'); fclose(fid);
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return
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end
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end
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kunnossa = 1;
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fclose(fid);
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%------------------------------------------------------
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function [data, popnames] = lueGenePopData(tiedostonNimi)
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fid = fopen(tiedostonNimi);
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line = fgetl(fid); %ensimmäinen rivi
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line = fgetl(fid); %toinen rivi
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count = rivinSisaltamienMjonojenLkm(line);
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line = fgetl(fid);
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lokusRiveja = 1;
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while (testaaPop(line)==0)
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lokusRiveja = lokusRiveja+1;
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line = fgetl(fid);
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end
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if lokusRiveja>1
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nloci = lokusRiveja;
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else
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nloci = count;
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end
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popnames = cell(10,2);
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data = zeros(100, nloci+1);
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nimienLkm=0;
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ninds=0;
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poimiNimi=1;
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digitFormat = -1;
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while line ~= -1
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line = fgetl(fid);
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if poimiNimi==1
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%Edellinen rivi oli 'pop'
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nimienLkm = nimienLkm+1;
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ninds = ninds+1;
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if nimienLkm>size(popnames,1);
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popnames = [popnames; cell(10,2)];
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end
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nimi = lueNimi(line);
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if digitFormat == -1
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digitFormat = selvitaDigitFormat(line);
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divider = 10^digitFormat;
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end
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popnames{nimienLkm, 1} = {nimi}; %Näin se on greedyMix:issäkin?!?
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popnames{nimienLkm, 2} = ninds;
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poimiNimi=0;
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data = addAlleles(data, ninds, line, divider);
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elseif testaaPop(line)
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poimiNimi = 1;
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elseif line ~= -1
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ninds = ninds+1;
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data = addAlleles(data, ninds, line, divider);
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end
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end
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data = data(1:ninds*2,:);
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popnames = popnames(1:nimienLkm,:);
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fclose(fid);
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%-------------------------------------------------------
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function nimi = lueNimi(line)
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%Palauttaa line:n alusta sen osan, joka on ennen pilkkua.
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n = 1;
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merkki = line(n);
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nimi = '';
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while ~isequal(merkki,',')
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nimi = [nimi merkki];
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n = n+1;
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merkki = line(n);
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end
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%-------------------------------------------------------
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function df = selvitaDigitFormat(line)
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% line on ensimmäinen pop-sanan jälkeinen rivi
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% Genepop-formaatissa olevasta datasta. funktio selvittää
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% rivin muodon perusteella, ovatko datan alleelit annettu
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% 2 vai 3 numeron avulla.
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n = 1;
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merkki = line(n);
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while ~isequal(merkki,',')
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n = n+1;
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merkki = line(n);
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end
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while ~any(merkki == '0123456789');
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n = n+1;
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merkki = line(n);
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end
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numeroja = 0;
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while any(merkki == '0123456789');
|
||||
numeroja = numeroja+1;
|
||||
n = n+1;
|
||||
merkki = line(n);
|
||||
end
|
||||
|
||||
df = numeroja/2;
|
||||
|
||||
|
||||
%------------------------------------------------------
|
||||
|
||||
|
||||
function count = rivinSisaltamienMjonojenLkm(line)
|
||||
% Palauttaa line:n sisältämien mjonojen lukumäärän.
|
||||
% Mjonojen välissä täytyy olla välilyönti.
|
||||
count = 0;
|
||||
pit = length(line);
|
||||
tila = 0; %0, jos odotetaan välilyöntejä, 1 jos odotetaan muita merkkejä
|
||||
for i=1:pit
|
||||
merkki = line(i);
|
||||
if (isspace(merkki) & tila==0)
|
||||
%Ei tehdä mitään.
|
||||
elseif (isspace(merkki) & tila==1)
|
||||
tila = 0;
|
||||
elseif (~isspace(merkki) & tila==0)
|
||||
tila = 1;
|
||||
count = count+1;
|
||||
elseif (~isspace(merkki) & tila==1)
|
||||
%Ei tehdä mitään
|
||||
end
|
||||
end
|
||||
|
||||
%-------------------------------------------------------
|
||||
|
||||
function pal = testaaPop(rivi)
|
||||
% pal=1, mikäli rivi alkaa jollain seuraavista
|
||||
% kirjainyhdistelmistä: Pop, pop, POP. Kaikissa muissa
|
||||
% tapauksissa pal=0.
|
||||
|
||||
if length(rivi)<3
|
||||
pal = 0;
|
||||
return
|
||||
end
|
||||
if (all(rivi(1:3)=='Pop') | ...
|
||||
all(rivi(1:3)=='pop') | ...
|
||||
all(rivi(1:3)=='POP'))
|
||||
pal = 1;
|
||||
return
|
||||
else
|
||||
pal = 0;
|
||||
return
|
||||
end
|
||||
|
||||
%-----------------------------------------------------------------------------------
|
||||
|
||||
|
||||
function [sumcounts, counts, logml] = ...
|
||||
initialCounts(partition, data, npops, rowsFromInd, noalle)
|
||||
|
||||
nloci=size(data,2);
|
||||
ninds = size(data,1)/rowsFromInd;
|
||||
|
||||
counts = zeros(max(noalle),nloci,npops);
|
||||
sumcounts = zeros(npops,nloci);
|
||||
for i=1:npops
|
||||
for j=1:nloci
|
||||
havainnotLokuksessa = find(partition==i & data(:,j)>=0);
|
||||
sumcounts(i,j) = length(havainnotLokuksessa);
|
||||
for k=1:noalle(j)
|
||||
alleleCode = k;
|
||||
N_ijk = length(find(data(havainnotLokuksessa,j)==alleleCode));
|
||||
counts(k,j,i) = N_ijk;
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
initializeGammaln(ninds, rowsFromInd, max(noalle));
|
||||
|
||||
logml = computeLogml(counts, sumcounts, noalle, data, rowsFromInd);
|
||||
|
||||
|
||||
%-----------------------------------------------------------------------
|
||||
|
||||
|
||||
function logml=computeLogml(counts, sumcounts, noalle, data, rowsFromInd)
|
||||
nloci = size(counts,2);
|
||||
npops = size(counts,3);
|
||||
adjnoalle = zeros(max(noalle),nloci);
|
||||
for j=1:nloci
|
||||
adjnoalle(1:noalle(j),j)=noalle(j);
|
||||
if (noalle(j)<max(noalle))
|
||||
adjnoalle(noalle(j)+1:end,j)=1;
|
||||
end
|
||||
end
|
||||
|
||||
%logml2 = sum(sum(sum(gammaln(counts+repmat(adjprior,[1 1 npops]))))) ...
|
||||
% - npops*sum(sum(gammaln(adjprior))) - ...
|
||||
% sum(sum(gammaln(1+sumcounts)));
|
||||
%logml = logml2;
|
||||
|
||||
global GAMMA_LN;
|
||||
rowsInG = size(data,1)+rowsFromInd;
|
||||
|
||||
logml = sum(sum(sum(GAMMA_LN(counts+1 + repmat(rowsInG*(adjnoalle-1),[1 1 npops]))))) ...
|
||||
- npops*sum(sum(GAMMA_LN(1, adjnoalle))) ...
|
||||
-sum(sum(GAMMA_LN(sumcounts+1,1)));
|
||||
|
||||
|
||||
%--------------------------------------------------------------------------
|
||||
|
||||
|
||||
function initializeGammaln(ninds, rowsFromInd, maxAlleles)
|
||||
%Alustaa GAMMALN muuttujan s.e. GAMMALN(i,j)=gammaln((i-1) + 1/j)
|
||||
global GAMMA_LN;
|
||||
GAMMA_LN = zeros((1+ninds)*rowsFromInd, maxAlleles);
|
||||
for i=1:(ninds+1)*rowsFromInd
|
||||
for j=1:maxAlleles
|
||||
GAMMA_LN(i,j)=gammaln((i-1) + 1/j);
|
||||
end
|
||||
end
|
||||
|
||||
%--------------------------------------------------------
|
||||
|
||||
|
||||
function data = addAlleles(data, ind, line, divider)
|
||||
% Lisaa BAPS-formaatissa olevaan datataulukkoon
|
||||
% yksilöä ind vastaavat rivit. Yksilön alleelit
|
||||
% luetaan genepop-formaatissa olevasta rivistä
|
||||
% line. Jos data on 3 digit formaatissa on divider=1000.
|
||||
% Jos data on 2 digit formaatissa on divider=100.
|
||||
|
||||
nloci = size(data,2)-1;
|
||||
if size(data,1) < 2*ind
|
||||
data = [data; zeros(100,nloci+1)];
|
||||
end
|
||||
|
||||
k=1;
|
||||
merkki=line(k);
|
||||
while ~isequal(merkki,',')
|
||||
k=k+1;
|
||||
merkki=line(k);
|
||||
end
|
||||
line = line(k+1:end);
|
||||
clear k; clear merkki;
|
||||
|
||||
alleeliTaulu = sscanf(line,'%d');
|
||||
|
||||
if length(alleeliTaulu)~=nloci
|
||||
disp('Incorrect data format.');
|
||||
end
|
||||
|
||||
for j=1:nloci
|
||||
ekaAlleeli = floor(alleeliTaulu(j)/divider);
|
||||
if ekaAlleeli==0 ekaAlleeli=-999; end;
|
||||
tokaAlleeli = rem(alleeliTaulu(j),divider);
|
||||
if tokaAlleeli==0 tokaAlleeli=-999; end
|
||||
|
||||
data(2*ind-1,j) = ekaAlleeli;
|
||||
data(2*ind,j) = tokaAlleeli;
|
||||
end
|
||||
|
||||
data(2*ind-1,end) = ind;
|
||||
data(2*ind,end) = ind;
|
||||
Loading…
Add table
Add a link
Reference in a new issue