Added computeAllFreqs2 function
This commit is contained in:
Waldir Leoncio
parent
d8df7fcb9e
commit
70528756fc
3 changed files with 50 additions and 41 deletions
56
R/admix1.R
56
R/admix1.R
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@ -5,7 +5,7 @@
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admix1 <- function(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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# if (filename==0 & pathname==0), return;
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# if (filename==0 & pathname==0), return;
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# else
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# disp('---------------------------------------------------');
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# disp(['Reading mixture result from: ',[pathname filename],'...']);
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@ -13,7 +13,7 @@ admix1 <- function(tietue) {
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# pause(0.0001);
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# h0 = findobj('Tag','filename1_text');
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# set(h0,'String',filename); clear h0;
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# struct_array = load([pathname filename]);
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# if isfield(struct_array,'c') #Matlab versio
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# c = struct_array.c;
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@ -31,7 +31,7 @@ admix1 <- function(tietue) {
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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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# (strcmp(c.mixtureType,'linear_mix') | ...
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# strcmp(c.mixtureType,'codon_mix')) # if the mixture is from a linkage model
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@ -40,7 +40,7 @@ admix1 <- function(tietue) {
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# linkage_admix(c);
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# return
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# end
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# PARTITION = c.PARTITION; COUNTS = c.COUNTS; SUMCOUNTS = c.SUMCOUNTS;
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# alleleCodes = c.alleleCodes; adjprior = c.adjprior; popnames = c.popnames;
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# rowsFromInd = c.rowsFromInd; data = c.data; npops = c.npops; noalle = c.noalle;
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@ -148,7 +148,7 @@ admix1 <- function(tietue) {
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# for iterationNum = 1:iterationCount
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# disp(['Iter: ' num2str(iterationNum)]);
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# allfreqs = simulateAllFreqs(noalle); # Allele frequencies on this iteration.
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# for ind=to_investigate
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# #disp(num2str(ind));
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# omaFreqs = computePersonalAllFreqs(ind, data, allfreqs, rowsFromInd);
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@ -172,7 +172,7 @@ admix1 <- function(tietue) {
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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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# 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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@ -227,23 +227,23 @@ admix1 <- function(tietue) {
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# for pop = admix_populaatiot'
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# for level = 1:n_missing_levels(pop)
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# potential_inds_in_this_pop_and_level = ...
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# find(PARTITION==pop & missing_level_partition==level &...
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# likelihood>3); # Potential admix individuals here.
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# if ~isempty(potential_inds_in_this_pop_and_level)
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# #refData = simulateIndividuals(nrefIndsInPop,rowsFromInd,allfreqs);
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# refData = simulateIndividuals(nrefIndsInPop, rowsFromInd, allfreqs, ...
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# pop, missing_levels(pop,level));
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# disp(['Analysing the reference individuals from pop ' num2str(pop) ' (level ' num2str(level) ').']);
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# refProportions = zeros(nrefIndsInPop,npops);
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# for iter = 1:iterationCountRef
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# #disp(['Iter: ' num2str(iter)]);
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# allfreqs = simulateAllFreqs(noalle);
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# for ind = 1:nrefIndsInPop
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# omaFreqs = computePersonalAllFreqs(ind, refData, allfreqs, rowsFromInd);
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# osuusTaulu = zeros(1,npops);
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@ -312,7 +312,7 @@ admix1 <- function(tietue) {
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# end
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# end
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# tulostaAdmixtureTiedot(proportionsIt, uskottavuus, alaRaja, iterationCount);
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# tulostaAdmixtureTiedot(proportionsIt, uskottavuus, alaRaja, iterationCount);
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# viewPartition(proportionsIt, popnames);
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@ -335,7 +335,7 @@ admix1 <- function(tietue) {
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# if (~isstruct(tietue))
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# c.proportionsIt = proportionsIt;
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# c.proportionsIt = proportionsIt;
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# c.pvalue = uskottavuus; # Added by Jing
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# c.mixtureType = 'admix'; # Jing
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# c.admixnpops = npops;
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@ -355,7 +355,7 @@ admix1 <- function(tietue) {
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# function [npops] = poistaLiianPienet(npops, rowsFromInd, alaraja)
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# % Muokkaa tulokset muotoon, jossa outlier yksilöt on
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# % poistettu. Tarkalleen ottaen poistaa ne populaatiot,
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# % poistettu. Tarkalleen ottaen poistaa ne populaatiot,
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# % joissa on vähemmän kuin 'alaraja':n verran yksilöit?
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# global PARTITION;
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@ -400,30 +400,4 @@ admix1 <- function(tietue) {
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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 allFreqs = computeAllFreqs2(noalle)
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# % Lisää a priori jokaista alleelia
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# % joka populaation joka lokukseen j 1/noalle(j) verran.
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# global COUNTS;
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# global SUMCOUNTS;
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# max_noalle = size(COUNTS,1);
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# nloci = size(COUNTS,2);
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# npops = size(COUNTS,3);
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# sumCounts = SUMCOUNTS+ones(size(SUMCOUNTS));
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# sumCounts = reshape(sumCounts', [1, nloci, npops]);
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# sumCounts = repmat(sumCounts, [max_noalle, 1 1]);
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# prioriAlleelit = zeros(max_noalle,nloci);
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# for j=1:nloci
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# prioriAlleelit(1:noalle(j),j) = 1/noalle(j);
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# end
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# prioriAlleelit = repmat(prioriAlleelit, [1,1,npops]);
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# counts = COUNTS + prioriAlleelit;
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# allFreqs = counts./sumCounts;
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# global POP_LOGML; POP_LOGML = [];
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23
R/computeAllFreqs2.R
Normal file
23
R/computeAllFreqs2.R
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@ -0,0 +1,23 @@
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#' @title Compute all freqs - version 2
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#' @description Lisää a priori jokaista alleelia joka populaation joka lokukseen
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#' j 1/noalle(j) verran.
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computeAllFreqs2 <- function (noalle, COUNTS = matrix(NA, 0, 0),
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SUMCOUNTS = sum(COUNTS)) {
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max_noalle <- size(COUNTS, 1)
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nloci <- size(COUNTS,2)
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npops <- size(COUNTS,3)
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sumCounts <- SUMCOUNTS + ones(size(SUMCOUNTS))
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sumCounts <- reshape(t(sumCounts), c(1, nloci, npops))
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sumCounts <- repmat(sumCounts, c(max_noalle, 1, 1))
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prioriAlleelit <- zeros(max_noalle, nloci)
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for (j in 1:nloci) {
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prioriAlleelit[1:noalle[j], j] <- 1 / noalle[j]
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}
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prioriAlleelit <- repmat(prioriAlleelit, c(1, 1, npops))
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counts <- COUNTS + prioriAlleelit
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allFreqs <- counts / sumCounts
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return(allFreqs)
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}
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12
man/computeAllFreqs2.Rd
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12
man/computeAllFreqs2.Rd
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@ -0,0 +1,12 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/computeAllFreqs2.R
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\name{computeAllFreqs2}
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\alias{computeAllFreqs2}
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\title{Compute all freqs - version 2}
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\usage{
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computeAllFreqs2(noalle, COUNTS = matrix(NA, 0, 0), SUMCOUNTS = sum(COUNTS))
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}
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\description{
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Lisää a priori jokaista alleelia joka populaation joka lokukseen
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j 1/noalle(j) verran.
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}
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