Examples with GeneSet org.baderlab.csplugins.enrichmentmap.model.GeneSet used on opensource projects

Example 11 with GeneSet

use of org.baderlab.csplugins.enrichmentmap.model.GeneSet in project EnrichmentMapApp by BaderLab.

the class CreateGMTEnrichmentMapTask method buildEnrichmentMap.

public void buildEnrichmentMap() {
    dataset.setMethod(Method.Generic);
    // in this case all the genesets are of interest
    dataset.setGeneSetsOfInterest(dataset.getSetOfGeneSets());
    Map<String, GeneSet> currentSets = dataset.getSetOfGeneSets().getGeneSets();
    // create an new Set of Enrichment Results                
    SetOfEnrichmentResults setOfEnrichments = new SetOfEnrichmentResults();
    Map<String, EnrichmentResult> currentEnrichments = setOfEnrichments.getEnrichments();
    // need also to put all genesets into enrichment results
    for (Iterator<String> i = currentSets.keySet().iterator(); i.hasNext(); ) {
        String geneset1Name = i.next();
        GeneSet gs = currentSets.get(geneset1Name);
        GenericResult tempResult = new GenericResult(gs.getName(), gs.getDescription(), 0.01, gs.getGenes().size());
        currentEnrichments.put(gs.getName(), tempResult);
    }
    dataset.setEnrichments(setOfEnrichments);
}

Example 12 with GeneSet

use of org.baderlab.csplugins.enrichmentmap.model.GeneSet in project EnrichmentMapApp by BaderLab.

the class GMTFileReaderTask method parse.

public void parse() throws IOException, InterruptedException {
    try (BufferedReader reader = new BufferedReader(new FileReader(gmtFileName))) {
        for (String line; (line = reader.readLine()) != null; ) {
            if (cancelled) {
                throw new InterruptedException();
            }
            GeneSet gs = readGeneSet(map, line);
            if (gs != null && setOfgenesets != null) {
                Map<String, GeneSet> genesets = setOfgenesets.getGeneSets();
                genesets.put(gs.getName(), gs);
            }
        }
    }
}

Example 13 with GeneSet

use of org.baderlab.csplugins.enrichmentmap.model.GeneSet in project EnrichmentMapApp by BaderLab.

the class ParseBingoEnrichmentResults method parseLines.

@Override
public void parseLines(List<String> lines, EMDataSet dataset, TaskMonitor taskMonitor) {
    if (taskMonitor == null)
        taskMonitor = new NullTaskMonitor();
    taskMonitor.setTitle("Parsing Bingo Enrichment Result file");
    //with Bingo results there are no genesets defined.  first pass through the file
    // needs to parse the genesets
    //the bingo file has 20 lines of info at the top of the file before you get to results.
    //parameters that can be extracted from Bingo files:
    //GO-ID	p-value	corr p-value	x	n	X	N	Description	Genes in test set
    // (column 1 ) GO-Id - is just the numerical part of the GO term (does not contain GO:0000)
    //(column 2 ) p-value
    //(column 3 ) corr pvalue
    //(column 4 ) x - number of genes in the subset of interest with this annotation
    //(column 5 ) n - number of genes in the universe with this annotation
    //(column 6 ) X - number of genes in the subset
    //(column 7 ) N - number of genes in the universe
    //(column 8 ) Description - GO term name
    //(column 9 ) Gene in test set - a list of genes in the subset of interest that are annotated to this term
    // Column 8 is the geneset name
    // Column 9 is the list of genes in this geneset -- therefore pre-filtered.
    Map<String, GeneSet> genesets = dataset.getSetOfGeneSets().getGeneSets();
    //get the genes (which should also be empty
    EnrichmentMap map = dataset.getMap();
    Map<String, EnrichmentResult> results = dataset.getEnrichments().getEnrichments();
    int currentProgress = 0;
    int maxValue = lines.size();
    boolean FDR = true;
    taskMonitor.setStatusMessage("Parsing Generic Results file -" + maxValue + " rows");
    //skip the first l9 which just has the field names (start i=1)
    //check to see how many columns the data has
    //go through each line until we find the header line
    int k = 0;
    String line = lines.get(k);
    String[] tokens = line.split("\t");
    for (; k < lines.size(); k++) {
        line = lines.get(k);
        tokens = line.split("\t");
        int length = tokens.length;
        if ((length == 9) && tokens[0].equalsIgnoreCase("GO-ID") && tokens[8].equalsIgnoreCase("Genes in test set")) {
            break;
        }
    }
    if (k == lines.size())
        throw new IllegalThreadStateException("Bingo results file is missing data.");
    for (int i = k + 1; i < lines.size(); i++) {
        line = lines.get(i);
        tokens = line.split("\t");
        double pvalue = 1.0;
        double FDRqvalue = 1.0;
        GenericResult result;
        int gs_size = 0;
        double NES = 1.0;
        //The 8th column of the file is the name of the geneset
        final String name = tokens[7].toUpperCase().trim();
        //the 8th column of the file is the description
        final String description = tokens[7].toUpperCase();
        //when there are two different species it is possible that the gene set could
        //already exist in the set of genesets.  if it does exist then add the genes
        //in this set to the geneset
        ImmutableSet.Builder<Integer> builder = ImmutableSet.builder();
        if (genesets.containsKey(name))
            builder = builder.addAll(genesets.get(name).getGenes());
        String[] gene_tokens = tokens[8].split("\\|");
        //All subsequent fields in the list are the geneset associated with this geneset.
        for (int j = 0; j < gene_tokens.length; j++) {
            String gene = gene_tokens[j].toUpperCase();
            //if it is already in the hash then get its associated key and put it into the set of genes
            if (map.containsGene(gene)) {
                builder.add(map.getHashFromGene(gene));
            } else if (!gene.isEmpty()) {
                Integer hash = map.addGene(gene).get();
                builder.add(hash);
            }
        }
        //finished parsing that geneset
        //add the current geneset to the hashmap of genesets
        GeneSet gs = new GeneSet(name, description, builder.build());
        genesets.put(name, gs);
        //The 2nd column is the nominal p-value
        if (tokens[1].equalsIgnoreCase("")) {
        //do nothing
        } else {
            pvalue = Double.parseDouble(tokens[1]);
        }
        //the Count is the size of the geneset (restricted by the gene list)
        if (tokens[3].equalsIgnoreCase("")) {
        //do nothing
        } else {
            gs_size = Integer.parseInt(tokens[3]);
        }
        //Use the correct p-value - 3rd column
        if (tokens[2].equalsIgnoreCase("")) {
        //do nothing
        } else {
            FDRqvalue = Double.parseDouble(tokens[2]);
        }
        result = new GenericResult(name, description, pvalue, gs_size, FDRqvalue);
        // Calculate Percentage.  This must be a value between 0..100.
        int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
        taskMonitor.setProgress(percentComplete);
        currentProgress++;
        //check to see if the gene set has already been entered in the results
        //it is possible that one geneset will be in both phenotypes.
        //if it is already exists then we want to make sure the one retained is the result with the
        //lower p-value.
        //ticket #149
        GenericResult temp = (GenericResult) results.get(name);
        if (temp == null)
            results.put(name, result);
        else {
            if (result.getPvalue() < temp.getPvalue())
                results.put(name, result);
        }
    }
    if (FDR)
        dataset.getMap().getParams().setFDR(FDR);
}

Example 14 with GeneSet

use of org.baderlab.csplugins.enrichmentmap.model.GeneSet in project EnrichmentMapApp by BaderLab.

the class ParseDavidEnrichmentResults method parseLines.

/**
	 * Parse david enrichment results file
	 */
@Override
public void parseLines(List<String> lines, EMDataSet dataset, TaskMonitor taskMonitor) {
    if (taskMonitor == null)
        taskMonitor = new NullTaskMonitor();
    taskMonitor.setTitle("Parsing David Enrichment Result file");
    //with David results there are no genesets defined.  first pass through the file
    // needs to parse the genesets
    //parameters that can be extracted from David files:
    //Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
    // Count = number of genes in the geneset that came from the input list, number of genes in the genelist mapping toa specific term.
    // List Total - number of genes in the gene list mapping to the category (ie. GO Cellular component)
    // Pop Hits - number of genes in the background gene list mapping to a specific term
    // Pop total - number of gene s in the background gene list mapping to the category (i.e. Go Cellular Component)
    // Column 2 is the geneset name
    // Column 1 is the category (and can be used for the description)
    // Column 6 is the list of genes (from the loaded list) in this geneset -- therefore pre-filtered.
    Map<String, GeneSet> genesets = dataset.getSetOfGeneSets().getGeneSets();
    EnrichmentMap map = dataset.getMap();
    Map<String, EnrichmentResult> results = dataset.getEnrichments().getEnrichments();
    int currentProgress = 0;
    int maxValue = lines.size();
    taskMonitor.setStatusMessage("Parsing Generic Results file - " + maxValue + " rows");
    boolean FDR = true;
    //skip the first line which just has the field names (start i=1)
    //check to see how many columns the data has
    String line = lines.get(0);
    String[] tokens = line.split("\t");
    int length = tokens.length;
    if (length != 13)
        throw new IllegalThreadStateException("David results file is missing data.");
    for (int i = 1; i < lines.size(); i++) {
        line = lines.get(i);
        tokens = line.split("\t");
        double pvalue = 1.0;
        double FDRqvalue = 1.0;
        GenericResult result;
        int gs_size = 0;
        double NES = 1.0;
        //The second column of the file is the name of the geneset
        final String name = tokens[1].toUpperCase().trim();
        //the first column of the file is the description
        final String description = tokens[0].toUpperCase();
        //when there are two different species it is possible that the gene set could
        //already exist in the set of genesets.  if it does exist then add the genes
        //in this set to the geneset
        ImmutableSet.Builder<Integer> builder = ImmutableSet.builder();
        if (genesets.containsKey(name))
            builder = builder.addAll(genesets.get(name).getGenes());
        String[] gene_tokens = tokens[5].split(", ");
        //All subsequent fields in the list are the geneset associated with this geneset.
        for (int j = 0; j < gene_tokens.length; j++) {
            String gene = gene_tokens[j].toUpperCase();
            //if it is already in the hash then get its associated key and put it into the set of genes
            if (map.containsGene(gene)) {
                builder.add(map.getHashFromGene(gene));
            } else if (!gene.isEmpty()) {
                Integer hash = map.addGene(gene).get();
                builder.add(hash);
            }
        }
        //finished parsing that geneset
        //add the current geneset to the hashmap of genesets
        GeneSet gs = new GeneSet(name, description, builder.build());
        genesets.put(name, gs);
        //The 5th column is the nominal p-value
        if (tokens[4].equalsIgnoreCase("")) {
        //do nothing
        } else {
            pvalue = Double.parseDouble(tokens[4]);
        }
        //the Count is the size of the geneset (restricted by the gene list)
        if (tokens[2].equalsIgnoreCase("")) {
        //do nothing
        } else {
            gs_size = Integer.parseInt(tokens[2]);
        }
        //Use the Benjamini value for the fdr
        if (tokens[11].equalsIgnoreCase("")) {
        //do nothing
        } else {
            FDRqvalue = Double.parseDouble(tokens[11]);
        }
        result = new GenericResult(name, description, pvalue, gs_size, FDRqvalue);
        // Calculate Percentage.  This must be a value between 0..100.
        int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
        taskMonitor.setProgress(percentComplete);
        currentProgress++;
        //check to see if the gene set has already been entered in the results
        //it is possible that one geneset will be in both phenotypes.
        //if it is already exists then we want to make sure the one retained is the result with the
        //lower p-value.
        //ticket #149
        GenericResult temp = (GenericResult) results.get(name);
        if (temp == null)
            results.put(name, result);
        else {
            if (result.getPvalue() < temp.getPvalue())
                results.put(name, result);
        }
    }
    if (FDR)
        dataset.getMap().getParams().setFDR(FDR);
}