Translated handlePopData (#2)
This commit is contained in:
Waldir Leoncio
parent
9224c44cb6
commit
03db7f4124
4 changed files with 86 additions and 94 deletions
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@ -12,6 +12,7 @@ export(fgetl)
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export(fopen)
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export(greedyMix)
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export(handleData)
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export(handlePopData)
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export(initPopNames)
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export(laskeMuutokset4)
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export(learn_partition_modified)
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71
R/handlePopData.R
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71
R/handlePopData.R
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@ -0,0 +1,71 @@
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#' @title Handle Pop data
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#' @description The last column of the original data tells you which
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#' <missing translation> that line is from. The function changes the allele
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#' codes so that the codes for one locus have values between 1 and noalle[j].
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#' Before this change, an allele whose code is zero is changed.
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#' @param raw_data raw data
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#' @export
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handlePopData <- function(raw_data) {
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# Alkuperäisen datan viimeinen sarake kertoo, milt?yksilölt?
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# kyseinen rivi on peräisin. Funktio muuttaa alleelikoodit
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# siten, ett?yhden lokuksen j koodit saavat arvoja
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# välill?1, ,noalle(j). Ennen tät?muutosta alleeli, jonka
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# koodi on nolla muutetaan.
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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 (length(nollat) > 0) {
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isoinAlleeli <- max(max(dataApu)$maxs)$maxs
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dataApu[nollat] <- isoinAlleeli + 1
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data[, 1:nloci] <- dataApu
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}
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noalle <- zeros(1, nloci)
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alleelitLokuksessa <- cell(nloci, 1, expandable = TRUE)
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for (i in 1:nloci) {
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alleelitLokuksessaI <- sort(unique(data[, i]))
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alleelitLokuksessa[[i]] <- alleelitLokuksessaI[find(alleelitLokuksessaI >= 0)]
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noalle[i] <- length(alleelitLokuksessa[[i]])
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}
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alleleCodes <- zeros(unique(max(noalle)$maxs), nloci)
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for (i in 1:nloci) {
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alleelitLokuksessaI <- alleelitLokuksessa[[i]]
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puuttuvia <- unique(max(noalle)$maxs) - length(alleelitLokuksessaI)
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alleleCodes[, i] = c(alleelitLokuksessaI, zeros(puuttuvia, 1))
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}
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for (loc in 1:nloci) {
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for (all in 1:noalle[loc]) {
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data[find(data[ , loc] == alleleCodes[all, loc]), loc] <- all
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}
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}
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nind <- max(data[, ncol(data)])$maxs
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rows <- zeros(nind, 2)
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for (i in 1:nind) {
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rivit <- t(find(data[, ncol(data)] == i))
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rows[i, 1] <- min(rivit)$mins
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rows[i, 2] <- max(rivit)$maxs
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}
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newData <- data
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adjprior <- zeros(unique(max(noalle)$maxs), nloci)
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priorTerm <- 0
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for (j in 1:nloci) {
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adjprior[, j] <- c(repmat(1 / noalle[j], c(noalle[j], 1)), ones(unique(max(noalle)$maxs) - noalle[j], 1))
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priorTerm <- priorTerm + noalle[j] * log(gamma(1 / noalle[j]))
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}
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return(
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list(
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newData = newData,
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rows = rows,
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alleleCodes = alleleCodes,
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noalle = noalle,
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adjprior = adjprior,
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priorTerm = priorTerm
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)
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)
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}
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14
man/handlePopData.Rd
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14
man/handlePopData.Rd
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@ -0,0 +1,14 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/handlePopData.R
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\name{handlePopData}
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\alias{handlePopData}
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\title{Handle Pop data}
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\usage{
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handlePopData(raw_data)
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}
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\arguments{
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\item{raw_data}{raw data}
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}
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\description{
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The last column of the original data tells you which? that line is from. The function changes the allele codes so that the codes for one locus have values between 1,, Noah (j). Before this change, an allele whose code is zero is changed.
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}
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@ -251,100 +251,6 @@ else
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end
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end
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%--------------------------------------------------------------------------
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function [newData, rows, alleleCodes, noalle, adjprior, priorTerm] = handlePopData(raw_data)
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% Alkuperäisen datan viimeinen sarake kertoo, milt?yksilölt?
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% kyseinen rivi on peräisin. Funktio muuttaa alleelikoodit
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% siten, ett?yhden lokuksen j koodit saavat arvoja
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% välill?1,...,noalle(j). Ennen tät?muutosta alleeli, jonka
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% koodi on nolla muutetaan.
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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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%rows = cell(nind,1);
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rows = zeros(nind,2);
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for i=1:nind
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rivit = find(data(:,end)==i)';
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rows(i,1) = min(rivit);
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rows(i,2) = max(rivit);
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end
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newData = data;
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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 [Z,distances] = getPopDistancesByKL(adjprior)
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% Laskee populaatioille etäisyydet
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% käyttäen KL-divergenssi?
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global COUNTS;
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maxnoalle = size(COUNTS,1);
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nloci = size(COUNTS,2);
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npops = size(COUNTS,3);
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distances = zeros(nchoosek(npops,2),1);
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d = zeros(maxnoalle, nloci, npops);
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prior = adjprior;
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prior(find(prior==1))=0;
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nollia = find(all(prior==0)); %Lokukset, joissa oli havaittu vain yht?alleelia.
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prior(1,nollia)=1;
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for pop1 = 1:npops
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d(:,:,pop1) = (squeeze(COUNTS(:,:,pop1))+prior) ./ repmat(sum(squeeze(COUNTS(:,:,pop1))+prior),maxnoalle,1);
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%dist1(pop1) = (squeeze(COUNTS(:,:,pop1))+adjprior) ./ repmat((SUMCOUNTS(pop1,:)+adjprior), maxnoalle, 1);
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end
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pointer = 1;
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for pop1 = 1:npops-1
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for pop2 = pop1+1:npops
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dist1 = d(:,:,pop1); dist2 = d(:,:,pop2);
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div12 = sum(sum(dist1.*log2((dist1+10^-10) ./ (dist2+10^-10))))/nloci;
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div21 = sum(sum(dist2.*log2((dist2+10^-10) ./ (dist1+10^-10))))/nloci;
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div = (div12+div21)/2;
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distances(pointer) = div;
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pointer = pointer+1;
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end
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end
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Z=linkage(distances');
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%--------------------------------------------------------------------
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