Added translation of admix
This commit is contained in:
Waldir Leoncio
parent
25cbfe4ed3
commit
76c408613d
1 changed files with 367 additions and 315 deletions
682
R/admix1.R
682
R/admix1.R
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@ -1,49 +1,64 @@
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#' @title Admixture analysis
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#' @title Admixture analysis
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#' @param tietue record
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#' @param tietue a named record list
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#' @details If the record == -1, the mixture results file is loaded. Otherwise, will the required variables be retrieved from the record fields?
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#' @details If the record == -1, the mixture results file is loaded. Otherwise,
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#' will the required variables be retrieved from the record fields?
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#' `tietue`should contain the following elements: PARTITION, COUNTS, SUMCOUNTS,
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#' alleleCodes, adjprior, popnames, rowsFromInd, data, npops, noalle
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#' @export
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#' @export
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admix1 <- function(tietue) {
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admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
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COUNTS = matrix(NA, 0, 0), SUMCOUNTS = NA) {
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if (!is.list(tietue)) {
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if (!is.list(tietue)) {
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# c(filename, pathname) = uigetfile('*.mat', 'Load mixture result file');
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message('Load mixture result file. These are the files in this directory:')
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# if (filename==0 & pathname==0), return;
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print(list.files())
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# else
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pathname_filename <- file.choose()
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# disp('---------------------------------------------------');
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if (!file.exists(pathname_filename)) {
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# disp(['Reading mixture result from: ',[pathname filename],'...']);
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stop(
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# end
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"File ", pathname_filename,
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# pause(0.0001);
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" does not exist. Check spelling and location."
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# h0 = findobj('Tag','filename1_text');
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)
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# set(h0,'String',filename); clear h0;
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} else {
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cat('---------------------------------------------------\n');
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message('Reading mixture result from: ', pathname_filename, '...')
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}
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sys.sleep(0.0001) #ASK: what for?
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# struct_array = load([pathname filename]);
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# ASK: what is this supposed to do? What do graphic obj have to do here?
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# if isfield(struct_array,'c') #Matlab versio
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# h0 = findobj('Tag','filename1_text');
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# c = struct_array.c;
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# set(h0,'String',filename); clear h0;
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# if ~isfield(c,'PARTITION') | ~isfield(c,'rowsFromInd')
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# disp('Incorrect file format');
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# return
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# end
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# elseif isfield(struct_array,'PARTITION') #Mideva versio
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# c = struct_array;
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# if ~isfield(c,'rowsFromInd')
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# disp('Incorrect file format');
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# return
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# end
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# else
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# disp('Incorrect file format');
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# return;
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# end
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# if isfield(c, 'gene_lengths') && ...
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struct_array <- load(pathname_filename)
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# (strcmp(c.mixtureType,'linear_mix') | ...
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if (isfield(struct_array, 'c')) { #Matlab versio
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# strcmp(c.mixtureType,'codon_mix')) # if the mixture is from a linkage model
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c <- struct_array$c
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# # Redirect the call to the linkage admixture function.
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if (!isfield(c, 'PARTITION') | !isfield(c,'rowsFromInd')) {
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# c.data = noIndex(c.data,c.noalle); # call function noindex to remove the index column
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stop('Incorrect file format')
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# linkage_admix(c);
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}
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# return
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} else if (isfield(struct_array, 'PARTITION')) { #Mideva versio
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# end
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c <- struct_array
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if (!isfield(c,'rowsFromInd')) stop('Incorrect file format')
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} else {
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stop('Incorrect file format')
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}
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# PARTITION = c.PARTITION; COUNTS = c.COUNTS; SUMCOUNTS = c.SUMCOUNTS;
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if (isfield(c, 'gene_lengths') &
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# alleleCodes = c.alleleCodes; adjprior = c.adjprior; popnames = c.popnames;
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strcmp(c$mixtureType, 'linear_mix') |
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# rowsFromInd = c.rowsFromInd; data = c.data; npops = c.npops; noalle = c.noalle;
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strcmp(c$mixtureType, 'codon_mix')) { # if the mixture is from a linkage model
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# Redirect the call to the linkage admixture function.
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# call function noindex to remove the index column
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c$data <- noIndex(c$data, c$noalle)
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# linkage_admix(c) # ASK: translate this function to R or drop?
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# return
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stop("linkage_admix not implemented")
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}
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PARTITION <- c$PARTITION
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COUNTS <- c$COUNTS
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SUMCOUNTS <- c$SUMCOUNTS
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alleleCodes <- c$alleleCodes
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adjprior <- c$adjprior
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popnames <- c$popnames
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rowsFromInd <- c$rowsFromInd
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data <- c$data
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npops <- c$npops
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noalle <- c$noalle
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} else {
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} else {
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PARTITION <- tietue$PARTITION
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PARTITION <- tietue$PARTITION
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COUNTS <- tietue$COUNTS
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COUNTS <- tietue$COUNTS
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@ -57,297 +72,334 @@ admix1 <- function(tietue) {
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noalle <- tietue$noalle
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noalle <- tietue$noalle
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}
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}
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# answers = inputdlg({['Input the minimum size of a population that will'...
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answers <- inputdlg(
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# ' be taken into account when admixture is estimated.']},...
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prompt = paste(
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# 'Input minimum population size',[1],...
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"Input the minimum size of a population that will",
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# {'5'});
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"be taken into account when admixture is estimated."
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# if isempty(answers) return; end
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),
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# alaRaja = str2num(answers{1,1});
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definput = 5
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# [npops] = poistaLiianPienet(npops, rowsFromInd, alaRaja);
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)
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alaRaja <- as.num(answers)
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npops <- poistaLiianPienet(npops, rowsFromInd, alaRaja)
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# nloci = size(COUNTS,2);
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nloci <- size(COUNTS, 2)
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# ninds = size(data,1)/rowsFromInd;
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ninds <- size(data, 1) / rowsFromInd
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# answers = inputdlg({['Input number of iterations']},'Input',[1],{'50'});
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answers <- inputdlg('Input number of iterations', 50)
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# if isempty(answers) return; end
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if (isempty(answers)) return()
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# iterationCount = str2num(answers{1,1});
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iterationCount <- as.numeric(answers[1, 1]) # maybe [[]]?
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# answers = inputdlg({['Input number of reference individuals from each population']},'Input',[1],{'50'});
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answers <- inputdlg(
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# if isempty(answers) nrefIndsInPop = 50;
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prompt = 'Input number of reference individuals from each population',
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# else nrefIndsInPop = str2num(answers{1,1});
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definput = 50
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# end
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)
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if (isempty(answers)) {
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nrefIndsInPop <- 50
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} else {
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nrefIndsInPop <- as.numeric(answers[1, 1])
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}
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# answers = inputdlg({['Input number of iterations for reference individuals']},'Input',[1],{'10'});
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answers <- inputdlg(
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# if isempty(answers) return; end
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prompt = 'Input number of iterations for reference individuals',
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# iterationCountRef = str2num(answers{1,1});
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definput = 10
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)
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if (isempty(answers)) return()
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iterationCountRef <- as.numeric(answers[1, 1])
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# First calculate log-likelihood ratio for all individuals:
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likelihood <- zeros(ninds, 1)
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allfreqs <- computeAllFreqs2(noalle)
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for (ind in 1:ninds) {
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omaFreqs <- computePersonalAllFreqs(ind, data, allfreqs, rowsFromInd)
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osuusTaulu <- zeros(1, npops)
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if (PARTITION[ind] == 0) {
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# Yksil?on outlier
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} else if (PARTITION[ind] != 0) {
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if (PARTITION[ind] > 0) {
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osuusTaulu(PARTITION[ind]) <- 1
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} else {
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# Yksilöt, joita ei ole sijoitettu mihinkään koriin.
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arvot <- zeros(1, npops)
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for (q in 1:npops) {
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osuusTaulu <- zeros(1, npops)
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osuusTaulu[q] <- 1
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arvot[q] <- computeIndLogml(omaFreqs, osuusTaulu)
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}
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iso_arvo <- max(arvot)
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isoimman_indeksi <- match(max(arvot), arvot)
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osuusTaulu <- zeros(1, npops)
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osuusTaulu[isoimman_indeksi] <- 1
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PARTITION[ind] <- isoimman_indeksi
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}
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logml <- computeIndLogml(omaFreqs, osuusTaulu)
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logmlAlku <- logml
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for (osuus in c(0.5, 0.25, 0.05, 0.01)) {
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etsiResult <- etsiParas(osuus, osuusTaulu, omaFreqs, logml)
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osuusTaulu <- etsiResult[1]
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logml <- etsiResult[2]
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}
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logmlLoppu <- logml
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likelihood[ind] <- logmlLoppu - logmlAlku
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}
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}
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# Analyze further only individuals who have log-likelihood ratio larger than 3:
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to_investigate <- t(find(likelihood > 3))
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cat('Possibly admixed individuals:\n')
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for (i in 1:length(to_investigate)) {
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cat(as.character(to_investigate[i]))
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}
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cat(' ')
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cat('Populations for possibly admixed individuals:\n')
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admix_populaatiot <- unique(PARTITION[to_investigate])
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for (i in 1:length(admix_populaatiot)) {
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cat(as.character(admix_populaatiot[i]))
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}
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# THUS, there are two types of individuals, who will not be analyzed with
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# simulated allele frequencies: those who belonged to a mini-population
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# which was removed, and those who have log-likelihood ratio less than 3.
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# The value in the PARTITION for the first kind of individuals is 0. The
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# second kind of individuals can be identified, because they do not
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# belong to "to_investigate" array. When the results are presented, the
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# first kind of individuals are omitted completely, while the second kind
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# of individuals are completely put to the population, where they ended up
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# in the mixture analysis. These second type of individuals will have a
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# unit p-value.
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# # First calculate log-likelihood ratio for all individuals:
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# Simulate allele frequencies a given number of times and save the average
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# likelihood = zeros(ninds,1);
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# result to "proportionsIt" array.
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# allfreqs = computeAllFreqs2(noalle);
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# for ind = 1:ninds
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# omaFreqs = computePersonalAllFreqs(ind, data, allfreqs, rowsFromInd);
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# osuusTaulu = zeros(1,npops);
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# if PARTITION(ind)==0
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# # Yksil?on outlier
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# elseif PARTITION(ind)~=0
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# if PARTITION(ind)>0
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# osuusTaulu(PARTITION(ind)) = 1;
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# else
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# # Yksilöt, joita ei ole sijoitettu mihinkään koriin.
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# arvot = zeros(1,npops);
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# for q=1:npops
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# osuusTaulu = zeros(1,npops);
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# osuusTaulu(q) = 1;
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# arvot(q) = computeIndLogml(omaFreqs, osuusTaulu);
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# end
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# [iso_arvo, isoimman_indeksi] = max(arvot);
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# osuusTaulu = zeros(1,npops);
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# osuusTaulu(isoimman_indeksi) = 1;
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# PARTITION(ind)=isoimman_indeksi;
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# end
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# logml = computeIndLogml(omaFreqs, osuusTaulu);
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# logmlAlku = logml;
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# for osuus = [0.5 0.25 0.05 0.01]
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# [osuusTaulu, logml] = etsiParas(osuus, osuusTaulu, omaFreqs, logml);
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# end
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# logmlLoppu = logml;
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# likelihood(ind) = logmlLoppu-logmlAlku;
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# end
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# end
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# # Analyze further only individuals who have log-likelihood ratio larger than 3:
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proportionsIt <- zeros(ninds, npops)
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# to_investigate = (find(likelihood>3))';
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for (iterationNum in 1:iterationCount) {
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# disp('Possibly admixed individuals: ');
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cat('Iter:', as.character(iterationNum))
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# for i = 1:length(to_investigate)
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allfreqs <- simulateAllFreqs(noalle) # Allele frequencies on this iteration.
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# disp(num2str(to_investigate(i)));
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# end
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# disp(' ');
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# disp('Populations for possibly admixed individuals: ');
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# admix_populaatiot = unique(PARTITION(to_investigate));
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# for i = 1:length(admix_populaatiot)
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# disp(num2str(admix_populaatiot(i)));
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# end
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# # THUS, there are two types of individuals, who will not be analyzed with
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for (ind in to_investigate) {
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# # simulated allele frequencies: those who belonged to a mini-population
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#disp(num2str(ind));
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# # which was removed, and those who have log-likelihood ratio less than 3.
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omaFreqs <- computePersonalAllFreqs(
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# # The value in the PARTITION for the first kind of individuals is 0. The
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ind, data, allfreqs, rowsFromInd
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# # second kind of individuals can be identified, because they do not
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)
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# # belong to "to_investigate" array. When the results are presented, the
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osuusTaulu = zeros(1, npops)
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# # first kind of individuals are omitted completely, while the second kind
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if (PARTITION[ind] == 0) {
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# # of individuals are completely put to the population, where they ended up
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# Yksil?on outlier
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# # in the mixture analysis. These second type of individuals will have a
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} else if (PARTITION[ind] != 0) {
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# # unit p-value.
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if (PARTITION[ind] > 0) {
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osuusTaulu(PARTITION[ind]) <- 1
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} else {
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# Yksilöt, joita ei ole sijoitettu mihinkään koriin.
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arvot <- zeros(1, npops)
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for (q in 1:npops) {
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osuusTaulu <- zeros(1, npops)
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osuusTaulu[q] <- 1
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arvot[q] <- computeIndLogml(omaFreqs, osuusTaulu)
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}
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iso_arvo <- max(arvot)
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isoimman_indeksi <- match(max(arvot), arvot)
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osuusTaulu <- zeros(1, npops)
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osuusTaulu[isoimman_indeksi] <- 1
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PARTITION[ind] <- isoimman_indeksi
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}
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logml <- computeIndLogml(omaFreqs, osuusTaulu)
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for (osuus in c(0.5, 0.25, 0.05, 0.01)) {
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etsiResult <- etsiParas(osuus, osuusTaulu, omaFreqs, logml)
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osuusTaulu <- etsiResult[1]
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logml <- etsiResult[2]
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}
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}
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proportionsIt[ind, ] <- proportionsIt[ind, ] * (iterationNum - 1) +
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osuusTaulu
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proportionsIt[ind, ] <- proportionsIt[ind, ] / iterationNum
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}
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}
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#disp(['Creating ' num2str(nrefIndsInPop) ' reference individuals from ']);
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#disp('each population.');
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#allfreqs = simulateAllFreqs(noalle); # Simuloidaan alleelifrekvenssisetti
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allfreqs <- computeAllFreqs2(noalle); # Koitetaan tällaista.
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# # Simulate allele frequencies a given number of times and save the average
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# Initialize the data structures, which are required in taking the missing
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# # result to "proportionsIt" array.
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# data into account:
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n_missing_levels <- zeros(npops, 1) # number of different levels of "missingness" in each pop (max 3).
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missing_levels <- zeros(npops, 3) # the mean values for different levels.
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missing_level_partition <- zeros(ninds, 1) # level of each individual (one of the levels of its population).
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for (i in 1:npops) {
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inds <- find(PARTITION == i)
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# Proportions of non-missing data for the individuals:
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non_missing_data <- zeros(length(inds), 1)
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for (j in 1:length(inds)) {
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ind <- inds[j]
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non_missing_data[j] <- length(
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find(data[(ind - 1) * rowsFromInd + 1:ind * rowsFromInd, ] > 0)
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) / (rowsFromInd * nloci)
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}
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if (all(non_missing_data > 0.9)) {
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n_missing_levels[i] <- 1
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missing_levels[i, 1] <- mean(non_missing_data)
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missing_level_partition[inds] <- 1
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} else {
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# TODO: fix syntax
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# [ordered, ordering] = sort(non_missing_data);
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ordered <- ordering <- sort(non_missing_data)
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#part = learn_simple_partition(ordered, 0.05);
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|
part <- learn_partition_modified(ordered)
|
||||||
|
aux <- sortrows(cbind(part, ordering), 2)
|
||||||
|
part = aux[, 1]
|
||||||
|
missing_level_partition[inds]<- part
|
||||||
|
n_levels <- length(unique(part))
|
||||||
|
n_missing_levels[i] <- n_levels
|
||||||
|
for (j in 1:n_levels) {
|
||||||
|
missing_levels[i, j] <- mean(non_missing_data[find(part == j)])
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
# proportionsIt = zeros(ninds,npops);
|
# Create and analyse reference individuals for populations
|
||||||
# for iterationNum = 1:iterationCount
|
# with potentially admixed individuals:
|
||||||
# disp(['Iter: ' num2str(iterationNum)]);
|
refTaulu <- zeros(npops, 100, 3)
|
||||||
# allfreqs = simulateAllFreqs(noalle); # Allele frequencies on this iteration.
|
for (pop in t(admix_populaatiot)) {
|
||||||
|
|
||||||
# for ind=to_investigate
|
for (level in 1:n_missing_levels[pop]) {
|
||||||
# #disp(num2str(ind));
|
|
||||||
# omaFreqs = computePersonalAllFreqs(ind, data, allfreqs, rowsFromInd);
|
|
||||||
# osuusTaulu = zeros(1,npops);
|
|
||||||
# if PARTITION(ind)==0
|
|
||||||
# # Yksil?on outlier
|
|
||||||
# elseif PARTITION(ind)~=0
|
|
||||||
# if PARTITION(ind)>0
|
|
||||||
# osuusTaulu(PARTITION(ind)) = 1;
|
|
||||||
# else
|
|
||||||
# # Yksilöt, joita ei ole sijoitettu mihinkään koriin.
|
|
||||||
# arvot = zeros(1,npops);
|
|
||||||
# for q=1:npops
|
|
||||||
# osuusTaulu = zeros(1,npops);
|
|
||||||
# osuusTaulu(q) = 1;
|
|
||||||
# arvot(q) = computeIndLogml(omaFreqs, osuusTaulu);
|
|
||||||
# end
|
|
||||||
# [iso_arvo, isoimman_indeksi] = max(arvot);
|
|
||||||
# osuusTaulu = zeros(1,npops);
|
|
||||||
# osuusTaulu(isoimman_indeksi) = 1;
|
|
||||||
# PARTITION(ind)=isoimman_indeksi;
|
|
||||||
# end
|
|
||||||
# logml = computeIndLogml(omaFreqs, osuusTaulu);
|
|
||||||
|
|
||||||
# for osuus = [0.5 0.25 0.05 0.01]
|
potential_inds_in_this_pop_and_level <-
|
||||||
# [osuusTaulu, logml] = etsiParas(osuus, osuusTaulu, omaFreqs, logml);
|
find(
|
||||||
# end
|
PARTITION == pop & missing_level_partition == level &
|
||||||
# end
|
likelihood > 3
|
||||||
# proportionsIt(ind,:) = proportionsIt(ind,:).*(iterationNum-1) + osuusTaulu;
|
) # Potential admix individuals here.
|
||||||
# proportionsIt(ind,:) = proportionsIt(ind,:)./iterationNum;
|
|
||||||
# end
|
|
||||||
# end
|
|
||||||
|
|
||||||
# #disp(['Creating ' num2str(nrefIndsInPop) ' reference individuals from ']);
|
if (!isempty(potential_inds_in_this_pop_and_level)) {
|
||||||
# #disp('each population.');
|
|
||||||
|
|
||||||
# #allfreqs = simulateAllFreqs(noalle); # Simuloidaan alleelifrekvenssisetti
|
#refData = simulateIndividuals(nrefIndsInPop,rowsFromInd,allfreqs);
|
||||||
# allfreqs = computeAllFreqs2(noalle); # Koitetaan tällaista.
|
refData <- simulateIndividuals(
|
||||||
|
nrefIndsInPop, rowsFromInd, allfreqs, pop,
|
||||||
|
missing_levels[pop, level]
|
||||||
|
)
|
||||||
|
|
||||||
|
cat(
|
||||||
|
'Analysing the reference individuals from pop', pop,
|
||||||
|
'(level', level, ').'
|
||||||
|
)
|
||||||
|
refProportions <- zeros(nrefIndsInPop, npops)
|
||||||
|
for (iter in 1:iterationCountRef) {
|
||||||
|
#disp(['Iter: ' num2str(iter)]);
|
||||||
|
allfreqs <- simulateAllFreqs(noalle)
|
||||||
|
|
||||||
|
for (ind in 1:nrefIndsInPop) {
|
||||||
|
omaFreqs <- computePersonalAllFreqs(
|
||||||
|
ind, refData, allfreqs, rowsFromInd
|
||||||
|
)
|
||||||
|
osuusTaulu <- zeros(1, npops)
|
||||||
|
osuusTaulu[pop] <- 1
|
||||||
|
logml <- computeIndLogml(omaFreqs, osuusTaulu)
|
||||||
|
for (osuus in c(0.5, 0.25, 0.05, 0.01)) {
|
||||||
|
etsiResult <- etsiParas(
|
||||||
|
osuus, osuusTaulu, omaFreqs, logml
|
||||||
|
)
|
||||||
|
osuusTaulu <- etsiResult[1]
|
||||||
|
logml <- etsiResult[2]
|
||||||
|
}
|
||||||
|
refProportions[ind, ] <-
|
||||||
|
refProportions[ind, ] * (iter - 1) + osuusTaulu
|
||||||
|
refProportions[ind, ] <- refProportions[ind, ] / iter
|
||||||
|
}
|
||||||
|
}
|
||||||
|
for (ind in 1:nrefIndsInPop) {
|
||||||
|
omanOsuus <- refProportions[ind, pop]
|
||||||
|
if (round(omanOsuus * 100) == 0) {
|
||||||
|
omanOsuus <- 0.01
|
||||||
|
}
|
||||||
|
if (abs(omanOsuus) < 1e-5) {
|
||||||
|
omanOsuus <- 0.01
|
||||||
|
}
|
||||||
|
refTaulu[pop, round(omanOsuus*100), level] <-
|
||||||
|
refTaulu[pop, round(omanOsuus*100),level] + 1
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
# Rounding of the results:
|
||||||
|
proportionsIt <- proportionsIt * 100
|
||||||
|
proportionsIt <- round(proportionsIt)
|
||||||
|
proportionsIt <- proportionsIt / 100
|
||||||
|
for (ind in 1:ninds) {
|
||||||
|
if (!any(to_investigate == ind)) {
|
||||||
|
if (PARTITION[ind] > 0) {
|
||||||
|
proportionsIt[ind, PARTITION[ind]] <- 1
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
# In case of a rounding error, the sum is made equal to unity by
|
||||||
|
# fixing the largest value.
|
||||||
|
if ((PARTITION[ind] > 0) & (sum(proportionsIt[ind, ]) != 1)) {
|
||||||
|
isoin <- max(proportionsIt[ind, ])
|
||||||
|
indeksi <- match(isoin, max(proportionsIt[ind, ]))
|
||||||
|
erotus <- sum(proportionsIt[ind, ]) - 1
|
||||||
|
proportionsIt[ind, indeksi] <- isoin - erotus
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
# Calculate p-value for each individual:
|
||||||
|
uskottavuus <- zeros(ninds, 1)
|
||||||
|
for (ind in 1:ninds) {
|
||||||
|
pop <- PARTITION[ind]
|
||||||
|
if (pop == 0) { # Individual is outlier
|
||||||
|
uskottavuus[ind] <- 1
|
||||||
|
} else if (isempty(find(to_investigate == ind))) {
|
||||||
|
# Individual had log-likelihood ratio<3
|
||||||
|
uskottavuus[ind] <- 1
|
||||||
|
} else {
|
||||||
|
omanOsuus <- proportionsIt[ind, pop]
|
||||||
|
if (abs(omanOsuus) < 1e-5) {
|
||||||
|
omanOsuus <- 0.01
|
||||||
|
}
|
||||||
|
if (round(omanOsuus*100)==0) {
|
||||||
|
omanOsuus <- 0.01
|
||||||
|
}
|
||||||
|
level <- missing_level_partition[ind]
|
||||||
|
refPienempia <- sum(refTaulu[pop, 1:round(100*omanOsuus), level])
|
||||||
|
uskottavuus[ind] <- refPienempia / nrefIndsInPop
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
# ASK: Remove? are these plotting functions?
|
||||||
|
tulostaAdmixtureTiedot(proportionsIt, uskottavuus, alaRaja, iterationCount)
|
||||||
|
viewPartition(proportionsIt, popnames)
|
||||||
|
|
||||||
|
talle = inputdlg('Do you want to save the admixture results? [Y/n]', 'y')
|
||||||
|
if (talle %in% c('y', 'Y', 'yes', 'Yes')) {
|
||||||
|
#waitALittle;
|
||||||
|
filename <- inputdlg(
|
||||||
|
'Save results as (file name):', 'admixture_results.rda'
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
# # Initialize the data structures, which are required in taking the missing
|
if (filename == 0) {
|
||||||
# # data into account:
|
# Cancel was pressed
|
||||||
# n_missing_levels = zeros(npops,1); # number of different levels of "missingness" in each pop (max 3).
|
return()
|
||||||
# missing_levels = zeros(npops,3); # the mean values for different levels.
|
} else { # copy 'baps4_output.baps' into the text file with the same name.
|
||||||
# missing_level_partition = zeros(ninds,1); # level of each individual (one of the levels of its population).
|
if (file.exists('baps4_output.baps')) {
|
||||||
# for i=1:npops
|
file.copy('baps4_output.baps', paste0(filename, '.txt'))
|
||||||
# inds = find(PARTITION==i);
|
file.remove('baps4_output.baps')
|
||||||
# # Proportions of non-missing data for the individuals:
|
}
|
||||||
# non_missing_data = zeros(length(inds),1);
|
}
|
||||||
# for j = 1:length(inds)
|
|
||||||
# ind = inds(j);
|
|
||||||
# non_missing_data(j) = length(find(data((ind-1)*rowsFromInd+1:ind*rowsFromInd,:)>0)) ./ (rowsFromInd*nloci);
|
|
||||||
# end
|
|
||||||
# if all(non_missing_data>0.9)
|
|
||||||
# n_missing_levels(i) = 1;
|
|
||||||
# missing_levels(i,1) = mean(non_missing_data);
|
|
||||||
# missing_level_partition(inds) = 1;
|
|
||||||
# else
|
|
||||||
# [ordered, ordering] = sort(non_missing_data);
|
|
||||||
# #part = learn_simple_partition(ordered, 0.05);
|
|
||||||
# part = learn_partition_modified(ordered);
|
|
||||||
# aux = sortrows([part ordering],2);
|
|
||||||
# part = aux(:,1);
|
|
||||||
# missing_level_partition(inds) = part;
|
|
||||||
# n_levels = length(unique(part));
|
|
||||||
# n_missing_levels(i) = n_levels;
|
|
||||||
# for j=1:n_levels
|
|
||||||
# missing_levels(i,j) = mean(non_missing_data(find(part==j)));
|
|
||||||
# end
|
|
||||||
# end
|
|
||||||
# end
|
|
||||||
|
|
||||||
# # Create and analyse reference individuals for populations
|
if (!isstruct(tietue)) {
|
||||||
# # with potentially admixed individuals:
|
c$proportionsIt <- proportionsIt
|
||||||
# refTaulu = zeros(npops,100,3);
|
c$pvalue <- uskottavuus # Added by Jing
|
||||||
# for pop = admix_populaatiot'
|
c$mixtureType <- 'admix' # Jing
|
||||||
|
c$admixnpops <- npops;
|
||||||
# for level = 1:n_missing_levels(pop)
|
save(c, file=filename)
|
||||||
|
} else {
|
||||||
# potential_inds_in_this_pop_and_level = ...
|
tietue$proportionsIt <- proportionsIt
|
||||||
# find(PARTITION==pop & missing_level_partition==level &...
|
tietue$pvalue <- uskottavuus; # Added by Jing
|
||||||
# likelihood>3); # Potential admix individuals here.
|
tietue$mixtureType <- 'admix'
|
||||||
|
tietue$admixnpops <- npops
|
||||||
# if ~isempty(potential_inds_in_this_pop_and_level)
|
save(tietue, file=filename)
|
||||||
|
}
|
||||||
# #refData = simulateIndividuals(nrefIndsInPop,rowsFromInd,allfreqs);
|
}
|
||||||
# refData = simulateIndividuals(nrefIndsInPop, rowsFromInd, allfreqs, ...
|
|
||||||
# pop, missing_levels(pop,level));
|
|
||||||
|
|
||||||
# disp(['Analysing the reference individuals from pop ' num2str(pop) ' (level ' num2str(level) ').']);
|
|
||||||
# refProportions = zeros(nrefIndsInPop,npops);
|
|
||||||
# for iter = 1:iterationCountRef
|
|
||||||
# #disp(['Iter: ' num2str(iter)]);
|
|
||||||
# allfreqs = simulateAllFreqs(noalle);
|
|
||||||
|
|
||||||
# for ind = 1:nrefIndsInPop
|
|
||||||
# omaFreqs = computePersonalAllFreqs(ind, refData, allfreqs, rowsFromInd);
|
|
||||||
# osuusTaulu = zeros(1,npops);
|
|
||||||
# osuusTaulu(pop)=1;
|
|
||||||
# logml = computeIndLogml(omaFreqs, osuusTaulu);
|
|
||||||
# for osuus = [0.5 0.25 0.05 0.01]
|
|
||||||
# [osuusTaulu, logml] = etsiParas(osuus, osuusTaulu, omaFreqs, logml);
|
|
||||||
# end
|
|
||||||
# refProportions(ind,:) = refProportions(ind,:).*(iter-1) + osuusTaulu;
|
|
||||||
# refProportions(ind,:) = refProportions(ind,:)./iter;
|
|
||||||
# end
|
|
||||||
# end
|
|
||||||
# for ind = 1:nrefIndsInPop
|
|
||||||
# omanOsuus = refProportions(ind,pop);
|
|
||||||
# if round(omanOsuus*100)==0
|
|
||||||
# omanOsuus = 0.01;
|
|
||||||
# end
|
|
||||||
# if abs(omanOsuus)<1e-5
|
|
||||||
# omanOsuus = 0.01;
|
|
||||||
# end
|
|
||||||
# refTaulu(pop, round(omanOsuus*100),level) = refTaulu(pop, round(omanOsuus*100),level)+1;
|
|
||||||
# end
|
|
||||||
# end
|
|
||||||
# end
|
|
||||||
# end
|
|
||||||
|
|
||||||
# # Rounding of the results:
|
|
||||||
# proportionsIt = proportionsIt.*100; proportionsIt = round(proportionsIt);
|
|
||||||
# proportionsIt = proportionsIt./100;
|
|
||||||
# for ind = 1:ninds
|
|
||||||
# if ~any(to_investigate==ind)
|
|
||||||
# if PARTITION(ind)>0
|
|
||||||
# proportionsIt(ind,PARTITION(ind))=1;
|
|
||||||
# end
|
|
||||||
# else
|
|
||||||
# # In case of a rounding error, the sum is made equal to unity by
|
|
||||||
# # fixing the largest value.
|
|
||||||
# if (PARTITION(ind)>0) & (sum(proportionsIt(ind,:)) ~= 1)
|
|
||||||
# [isoin,indeksi] = max(proportionsIt(ind,:));
|
|
||||||
# erotus = sum(proportionsIt(ind,:))-1;
|
|
||||||
# proportionsIt(ind,indeksi) = isoin-erotus;
|
|
||||||
# end
|
|
||||||
# end
|
|
||||||
# end
|
|
||||||
|
|
||||||
# # Calculate p-value for each individual:
|
|
||||||
# uskottavuus = zeros(ninds,1);
|
|
||||||
# for ind = 1:ninds
|
|
||||||
# pop = PARTITION(ind);
|
|
||||||
# if pop==0 # Individual is outlier
|
|
||||||
# uskottavuus(ind)=1;
|
|
||||||
# elseif isempty(find(to_investigate==ind))
|
|
||||||
# # Individual had log-likelihood ratio<3
|
|
||||||
# uskottavuus(ind)=1;
|
|
||||||
# else
|
|
||||||
# omanOsuus = proportionsIt(ind,pop);
|
|
||||||
# if abs(omanOsuus)<1e-5
|
|
||||||
# omanOsuus = 0.01;
|
|
||||||
# end
|
|
||||||
# if round(omanOsuus*100)==0
|
|
||||||
# omanOsuus = 0.01;
|
|
||||||
# end
|
|
||||||
# level = missing_level_partition(ind);
|
|
||||||
# refPienempia = sum(refTaulu(pop, 1:round(100*omanOsuus), level));
|
|
||||||
# uskottavuus(ind) = refPienempia / nrefIndsInPop;
|
|
||||||
# end
|
|
||||||
# end
|
|
||||||
|
|
||||||
# tulostaAdmixtureTiedot(proportionsIt, uskottavuus, alaRaja, iterationCount);
|
|
||||||
|
|
||||||
# viewPartition(proportionsIt, popnames);
|
|
||||||
|
|
||||||
# talle = questdlg(['Do you want to save the admixture results?'], ...
|
|
||||||
# 'Save results?','Yes','No','Yes');
|
|
||||||
# if isequal(talle,'Yes')
|
|
||||||
# #waitALittle;
|
|
||||||
# [filename, pathname] = uiputfile('*.mat','Save results as');
|
|
||||||
|
|
||||||
|
|
||||||
# if (filename == 0) & (pathname == 0)
|
|
||||||
# # Cancel was pressed
|
|
||||||
# return
|
|
||||||
# else # copy 'baps4_output.baps' into the text file with the same name.
|
|
||||||
# if exist('baps4_output.baps','file')
|
|
||||||
# copyfile('baps4_output.baps',[pathname filename '.txt'])
|
|
||||||
# delete('baps4_output.baps')
|
|
||||||
# end
|
|
||||||
# end
|
|
||||||
|
|
||||||
|
|
||||||
# if (~isstruct(tietue))
|
|
||||||
# c.proportionsIt = proportionsIt;
|
|
||||||
# c.pvalue = uskottavuus; # Added by Jing
|
|
||||||
# c.mixtureType = 'admix'; # Jing
|
|
||||||
# c.admixnpops = npops;
|
|
||||||
# # save([pathname filename], 'c');
|
|
||||||
# save([pathname filename], 'c', '-v7.3'); # added by Lu Cheng, 08.06.2012
|
|
||||||
# else
|
|
||||||
# tietue.proportionsIt = proportionsIt;
|
|
||||||
# tietue.pvalue = uskottavuus; # Added by Jing
|
|
||||||
# tietue.mixtureType = 'admix';
|
|
||||||
# tietue.admixnpops = npops;
|
|
||||||
# # save([pathname filename], 'tietue');
|
|
||||||
# save([pathname filename], 'tietue', '-v7.3'); # added by Lu Cheng, 08.06.2012
|
|
||||||
# end
|
|
||||||
# end
|
|
||||||
}
|
}
|
||||||
Loading…
Add table
Reference in a new issue