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geneSetRankEval.m
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geneSetRankEval.m
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%%% 27 Sep 2013
%%% calculate the ranksum p-value for a gene set within all genes
function [pValCorr_corrected, newSheetNames] = geneSetRankEval(filesDirectory, resultsDirectory, geneOfInterest, ...
structures, geneSetName, expType, allGenes, allExpNumbers, allExpPlanes)
[~, txt] = xlsread([filesDirectory 'gene sets/' geneSetName '.xlsx']);
geneSet = txt(2:end,1);
clear txt;
geneSetInd = find(ismember(allGenes, geneSet) == 1);
geneSetNames = allGenes(geneSetInd);
geneSetExpNo = allExpNumbers(geneSetInd);
geneSetExpPlanes = allExpPlanes(geneSetInd);
%%% create the outfile for this analysis
outDir = [resultsDirectory geneSetName];
if ~exist(outDir, 'dir')
mkdir(outDir);
end
if strcmp(expType, 'C')
outFile = [outDir '/' geneSetName '_' geneOfInterest{1} 'rank-pVal_C.xls'];
xlsDIR = [resultsDirectory 'xlsFiles/CoronalOnly/'];
gene_index = find(strcmpi(allGenes(1:4345), geneOfInterest) == 1);
extension = '_CoronalOnly';
nGenes = 4345;
elseif strcmp(expType, 'All')
outFile = [outDir '/' geneSetName '_' geneOfInterest{1} 'rank-pVal_All.xls'];
xlsDIR = [resultsDirectory 'xlsFiles/All/'];
gene_index = find(strcmpi(allGenes, geneOfInterest) == 1);
extension = '';
nGenes = 26022;
else
display('expType not defined correctly');
end
%%% find all experiments of the geneOfInterest
gene_experimentNos = allExpNumbers(gene_index);
gene_experimentPlanes = allExpPlanes(gene_index);
%%% loop on all the gene experiments
for experiment = 1 : length(gene_index)
newSheetNames{experiment} = [allGenes{gene_index(experiment)} '_' gene_experimentNos{experiment} '_' gene_experimentPlanes{experiment}];
%%% loop on all the structures in the structures list
for s = 1 : length(structures)
%%% load the file corresponding to the current structure and
%%% gene experiment
[num txt] = xlsread([xlsDIR geneOfInterest{1} '/' geneOfInterest{1} '_' structures{s} extension '.xls'], experiment);
rankedGenes = txt(3:end, 2);
rankedExpNo = num(1:end,3);
rankedExpPlane = txt(3:end, 4);
rankedCorrVals = num(1:end,5);
avgExpVals = num(1:end,7);
locScores = num(1:end,8);
% generate sorted gene lists based on the average expression
% and localization scores for the current structure
[sortedAvgExpVals sortingInd_avgExpVals] = sort(avgExpVals, 'descend');%%% watch out for tied ranks!!!
[sortedCLocScores sortingInd_locScores] = sort(locScores, 'descend');
clear txt; clear num;
% return the corr, avg. epression and the localization score
% for all the experiments of each gene
indecies = 0;
for g = 1 : length(geneSetNames)
% find the index of the gene within the ranked list
tempR = find(ismember(rankedGenes, geneSetNames{g}) == 1);
if ~isempty(tempR)
tempRE = find(rankedExpNo(tempR) == str2double(geneSetExpNo{g}));
if ~isempty(tempRE)
currGeneSetInd(g) = tempR(tempRE);
geneCorr(g) = rankedCorrVals(tempR(tempRE));
geneCorrRank(g) = tempR(tempRE);
geneAvgExp(g) = avgExpVals(tempR(tempRE));
geneExpRank(g) = sortingInd_avgExpVals(tempR(tempRE));
geneLocScore(g) = locScores(tempR(tempRE));
geneLocRank(g) = sortingInd_locScores(tempR(tempRE));
else
currGeneSetInd(g) = 0;
geneCorr(g) = 0;
geneCorrRank(g) = 0;
geneAvgExp(g) = 0;
geneExpRank(g) = 0;
geneLocScore(g) = 0;
geneLocRank(g) = 0;
end
else
currGeneSetInd(g) = 0;
geneCorr(g) = 0;
geneCorrRank(g) = 0;
geneAvgExp(g) = 0;
geneExpRank(g) = 0;
geneLocScore(g) = 0;
geneLocRank(g) = 0;
end
clear tempR;
end
clear g;
%%% clean the data!!!!!!!!!!!!
remRows = find(currGeneSetInd == 0);
currGeneSetInd(remRows) = [];
geneCorr(remRows) = [];
geneCorrRank(remRows) = [];
geneAvgExp(remRows) = [];
geneExpRank(remRows) = [];
geneLocScore(remRows) = [];
geneLocRank(remRows) = [];
%%% (1) calculate the ranksum pval based on correlation
tempCorrArr = rankedCorrVals;
tempCorrArr(currGeneSetInd) = [];
pValCorr(experiment,s) = ranksum(tempCorrArr, geneCorr);
%%% (1') prepare data for boxplot
if s == 1
labels = zeros(1,length(geneCorr))+s;
geneCorrPlot = geneCorr;
geneRankPlot = geneCorrRank;
else
labels = [labels zeros(1,length(geneCorr))+s];
geneCorrPlot = [geneCorrPlot geneCorr];
geneRankPlot = [geneRankPlot geneCorrRank];
end
%%% (2) calculate the sum of the ranks of the current gene set
corrSumOfRanks = sum(-log10(geneCorrRank/nGenes));
% %%% (3) plot a distribution of rank sums for random sets of genes
% %%% of the same size as the gene set of interest
% noRandSets = 10000;
% for rs = 1 : noRandSets
% clear inds; clear randCorrArr; clear tempTempCorrArr;
% inds = randperm(length(tempCorrArr), length(currGeneSetInd));
% randCorrArr = tempCorrArr(inds);
% tempTempCorrArr = tempCorrArr; tempTempCorrArr(inds) = [];
% randPValCorr(rs) = ranksum(tempTempCorrArr, randCorrArr);
% randCorrSumOfRanks(rs) = sum(-log10(inds/ nGenes));
% end
% f = figure('Visible', 'off');
% set(gcf,'units','normalized','outerposition',[0 0 1 1]);
% hold on
% subplot(1,2,1); hist(randCorrSumOfRanks, 1000); grid on
% line([corrSumOfRanks corrSumOfRanks], [0 50], 'linewidth', 3, 'color', 'red', 'linestyle', '--')
% text(corrSumOfRanks+2, 20, num2str(corrSumOfRanks), 'Color', 'r', 'FontWeight', 'bold', 'FontSize', 15, 'Rotation', 90)
% set(gca, 'XLim', [0 100]);
% set(gca, 'YLim', [0 60]);
% xlabel('Sum of the ranks', 'FontWeight', 'bold', 'FontSize', 15)
% ylabel('Frequency', 'FontWeight', 'bold', 'FontSize', 15)
% title({[allGenes{gene_index(experiment)} ' ' gene_experimentNos{experiment} ' ' gene_experimentPlanes{experiment}], ...
% structures{s}}, 'FontWeight', 'bold', 'FontSize', 15);
% subplot(1,2,2); hist(-log10(randPValCorr), 1000); grid on
% line([-log10(pValCorr(experiment,s)) -log10(pValCorr(experiment,s))], [0 80], 'linewidth', 3, 'color', 'red', 'linestyle', '--')
% text(-log10(pValCorr(experiment,s))+1, 40, num2str(pValCorr(experiment,s)), 'Color', 'r', 'FontWeight', 'bold', 'FontSize', 15, 'Rotation', 90)
% set(gca, 'XLim', [0 20]);
% set(gca, 'YLim', [0 120]);
% xlabel('-log_1_0(ranksum p-value)', 'FontWeight', 'bold', 'FontSize', 15)
% ylabel('Frequency', 'FontWeight', 'bold', 'FontSize', 15)
% title({[allGenes{gene_index(experiment)} ' ' gene_experimentNos{experiment} ' ' gene_experimentPlanes{experiment}], ...
% structures{s}}, 'FontWeight', 'bold', 'FontSize', 15);
% hold off
% saveas(f, [outDir '/' newSheetNames{experiment} '_' expType '_' structures{s} '_randomSet.fig']);
% saveas(f, [outDir '/' newSheetNames{experiment} '_' expType '_' structures{s} '_randomSet.jpg']);
end
clear offset; clear Workbook; clear sheet1; clear eActivesheetRange;
clear ri; clear r11; clear r2; clear r22; clear r3;
%%% correct for multiple testing
pValCorr_corrected(experiment,:) = multtest(pValCorr(experiment,:),'method','BH');
%%% plot boxplots of the correlations in different structures together
%%% with the corresponding p-value
% f = figure;
% subplot(2,1,1), notBoxPlot(geneCorrPlot, labels); grid on;
% ylabel('Correlation with Esr1', 'FontWeight', 'bold', 'FontSize', 15)
% set(gca, 'XTickLabel', structures, 'FontWeight', 'bold', 'xlim', [0 numel(structures)+1]);
% rotateXLabels(gca(), 45)
% % title([allGenes{gene_index(experiment)} ' ' gene_experimentNos{experiment} ' ' gene_experimentPlanes{experiment} ' - ' expType],...
% % 'FontWeight', 'bold', 'FontSize', 15);
% subplot(2,1,2), bar(-1*log10(pValCorr_corrected)); grid on;
% ylabel('- log_1_0 (p-value)', 'FontWeight', 'bold', 'FontSize', 15)
% set(gca, 'XTickLabel', structures, 'FontWeight', 'bold', ...
% 'XTick', 1:numel(structures), 'xlim', [0 numel(structures)+1], ...
% 'ylim', [0 8]);
% % rotateXLabels(gca(), 45)
% % title('Mann-Whitney U-test', 'FontWeight', 'bold', 'FontSize', 15);
% line([0 numel(structures)+1], [-log10(0.05) -log10(0.05)], 'LineWidth', 3, 'color', 'r')
% hold off
% saveas(f, [outDir '/' newSheetNames{experiment} '_' expType '_CorrelationAnalysis.fig']);
% saveas(f, [outDir '/' newSheetNames{experiment} '_' expType '_CorrelationAnalysis.jpg']);
end
% %%% write the results to excel
% xlswrite(outFile, structures, 1, 'B1');
% xlswrite(outFile, pValCorr, 1, 'B2');
% xlswrite(outFile, newSheetNames', 1, 'A2');