Examples with ProbeList uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList used on opensource projects

Example 66 with ProbeList

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList in project SeqMonk by s-andrews.

the class RandomFilter method generateProbeList.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Filters.ProbeFilter#generateProbeList()
	 */
@Override
protected void generateProbeList() {
    ProbeList newList = new ProbeList(startingList, "", "", "No value");
    Probe[] probes = startingList.getAllProbes();
    // This list is a sublist and is only used if we're generating more than one list
    ProbeList currentList = null;
    HashSet<Probe> seenProbes = new HashSet<Probe>();
    for (int i = 1; i <= numberOfListsToGenerate; i++) {
        if (numberOfListsToGenerate > 1) {
            currentList = new ProbeList(newList, "Random list " + i, listDescription(), null);
        }
        // Make a random set
        Collections.shuffle(Arrays.asList(probes));
        for (int j = 0; j < numberOfProbesPerList; j++) {
            if (cancel) {
                cancel = false;
                progressCancelled();
                return;
            }
            if (numberOfListsToGenerate == 1) {
                newList.addProbe(probes[j], null);
            } else {
                currentList.addProbe(probes[j], null);
                if (!seenProbes.contains(probes[j])) {
                    newList.addProbe(probes[j], null);
                    seenProbes.add(probes[j]);
                }
            }
        }
    }
    filterFinished(newList);
}

Example 67 with ProbeList

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList in project SeqMonk by s-andrews.

the class HeatmapProbeListWindow method actionPerformed.

/* (non-Javadoc)
	 * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
	 */
public void actionPerformed(ActionEvent ae) {
    if (ae.getActionCommand().equals("close")) {
        setVisible(false);
        dispose();
    } else if (ae.getActionCommand().equals("save_image")) {
        ImageSaver.saveImage(heatmapPanel);
    } else if (ae.getActionCommand().equals("cluster")) {
        if (clusterButton.getText().equals("Cluster Interactions")) {
            // First we need to make up an interaction cluster matrix which we
            // can then feed to the generic hierarchical clustering program
            InteractionClusterMatrix clusterMatrix = new InteractionClusterMatrix(matrix.filteredInteractions(), matrix.probeCount());
            clusterMatrix.addListener(new ProgressDialog(this, "HiC Interaction Clustering", clusterMatrix));
            clusterMatrix.addListener(this);
            clusterMatrix.startCorrelating();
            clusterButton.setEnabled(false);
        } else {
            matrix.setCluster(null);
            saveClustersButton.setEnabled(false);
            clusterButton.setText("Cluster Interactions");
        }
    } else if (ae.getActionCommand().equals("save_probes")) {
        ProbeList newList = matrix.createProbeListFromCurrentInteractions();
        // Ask for a name for the list
        String groupName = null;
        while (true) {
            groupName = (String) JOptionPane.showInputDialog(this, "Enter list name", "Found " + newList.getAllProbes().length + " probes", JOptionPane.QUESTION_MESSAGE, null, null, newList.name());
            if (groupName == null) {
                // Since the list will automatically have been added to
                // the ProbeList tree we actively need to delete it if
                // they choose to cancel at this point.
                newList.delete();
                // They cancelled
                return;
            }
            if (groupName.length() == 0)
                // Try again
                continue;
            break;
        }
        newList.setName(groupName);
    } else if (ae.getActionCommand().equals("save_clusters")) {
        if (matrix.cluster() == null)
            return;
        // Get a limit for how many probes per cluster
        String howManyProbes = JOptionPane.showInputDialog(this, "Minimum number of probes per cluster", "10");
        if (howManyProbes == null)
            return;
        int minProbes;
        try {
            minProbes = Integer.parseInt(howManyProbes);
        } catch (NumberFormatException nfe) {
            JOptionPane.showMessageDialog(this, howManyProbes + " was not an integer", "Error", JOptionPane.ERROR_MESSAGE);
            return;
        }
        ProbeList newList = matrix.createProbeListsFromClusters(minProbes, heatmapPanel.probeListPanel().currentYStartIndex(), heatmapPanel.probeListPanel().currentYEndIndex());
        // This was called before clustering had completed.
        if (newList == null)
            return;
        // Ask for a name for the list
        String groupName = null;
        while (true) {
            groupName = (String) JOptionPane.showInputDialog(this, "Enter list name", "Found " + newList.getAllProbes().length + " probes", JOptionPane.QUESTION_MESSAGE, null, null, newList.name());
            if (groupName == null) {
                // Since the list will automatically have been added to
                // the ProbeList tree we actively need to delete it if
                // they choose to cancel at this point.
                newList.delete();
                // They cancelled
                return;
            }
            if (groupName.length() == 0)
                // Try again
                continue;
            break;
        }
        newList.setName(groupName);
    } else if (ae.getActionCommand().equals("make_report")) {
        new InteractionReportOptions(SeqMonkApplication.getInstance(), new AnnotatedInteractionReport(SeqMonkApplication.getInstance().dataCollection(), matrix));
    }
}

Example 68 with ProbeList

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList in project SeqMonk by s-andrews.

the class BinomialFilterForRev method generateProbeList.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Filters.ProbeFilter#generateProbeList()
	 */
protected void generateProbeList() {
    boolean aboveOnly = false;
    boolean belowOnly = false;
    if (options.directionBox.getSelectedItem().equals("Above"))
        aboveOnly = true;
    else if (options.directionBox.getSelectedItem().equals("Below"))
        belowOnly = true;
    if (options.stringencyField.getText().length() == 0) {
        stringency = 0.05;
    } else {
        stringency = Double.parseDouble(options.stringencyField.getText());
    }
    if (options.minObservationsField.getText().length() == 0) {
        minObservations = 10;
    } else {
        minObservations = Integer.parseInt(options.minObservationsField.getText());
    }
    if (options.minDifferenceField.getText().length() == 0) {
        minPercentShift = 10;
    } else {
        minPercentShift = Integer.parseInt(options.minDifferenceField.getText());
    }
    useCurrentQuant = options.useCurrentQuantBox.isSelected();
    applyMultipleTestingCorrection = options.multiTestBox.isSelected();
    ProbeList newList;
    if (applyMultipleTestingCorrection) {
        newList = new ProbeList(startingList, "Filtered Probes", "", "Q-value");
    } else {
        newList = new ProbeList(startingList, "Filtered Probes", "", "P-value");
    }
    Probe[] probes = startingList.getAllProbes();
    // We need to create a set of mean end methylation values for all starting values
    // We found to the nearest percent so we'll end up with a set of 101 values (0-100)
    // which are the expected end points
    double[] expectedEnds = calculateEnds(probes);
    // They cancelled whilst calculating.
    if (expectedEnds == null)
        return;
    for (int i = 0; i < expectedEnds.length; i++) {
        System.err.println("" + i + "\t" + expectedEnds[i]);
    }
    // This is where we'll store any hits
    Vector<ProbeTTestValue> hits = new Vector<ProbeTTestValue>();
    BinomialTest bt = new BinomialTest();
    AlternativeHypothesis hypothesis = AlternativeHypothesis.TWO_SIDED;
    if (aboveOnly)
        hypothesis = AlternativeHypothesis.GREATER_THAN;
    if (belowOnly)
        hypothesis = AlternativeHypothesis.LESS_THAN;
    for (int p = 0; p < probes.length; p++) {
        if (p % 100 == 0) {
            progressUpdated("Processed " + p + " probes", p, probes.length);
        }
        if (cancel) {
            cancel = false;
            progressCancelled();
            return;
        }
        long[] reads = fromStore.getReadsForProbe(probes[p]);
        int forCount = 0;
        int revCount = 0;
        for (int r = 0; r < reads.length; r++) {
            if (SequenceRead.strand(reads[r]) == Location.FORWARD) {
                ++forCount;
            } else if (SequenceRead.strand(reads[r]) == Location.REVERSE) {
                ++revCount;
            }
        }
        if (forCount + revCount < minObservations)
            continue;
        int fromPercent = Math.round((forCount * 100f) / (forCount + revCount));
        // We need to calculate the confidence range for the from reads and work
        // out the most pessimistic value we could take as a starting value
        WilsonScoreInterval wi = new WilsonScoreInterval();
        ConfidenceInterval ci = wi.createInterval(forCount + revCount, forCount, 1 - stringency);
        // System.err.println("From percent="+fromPercent+" meth="+forCount+" unmeth="+revCount+" sig="+stringency+" ci="+ci.getLowerBound()*100+" - "+ci.getUpperBound()*100);
        reads = toStore.getReadsForProbe(probes[p]);
        forCount = 0;
        revCount = 0;
        for (int r = 0; r < reads.length; r++) {
            if (SequenceRead.strand(reads[r]) == Location.FORWARD) {
                ++forCount;
            } else if (SequenceRead.strand(reads[r]) == Location.REVERSE) {
                ++revCount;
            }
        }
        if (forCount + revCount < minObservations)
            continue;
        float toPercent = (forCount * 100f) / (forCount + revCount);
        // System.err.println("Observed toPercent is "+toPercent+ "from meth="+forCount+" unmeth="+revCount+" and true predicted is "+expectedEnds[Math.round(toPercent)]);
        // Find the most pessimistic fromPercent such that the expected toPercent is as close
        // to the observed value based on the confidence interval we calculated before.
        double worseCaseExpectedPercent = 0;
        double smallestTheoreticalToActualDiff = 100;
        // Just taking the abs diff can still leave us with a closest value which is still
        // quite far from where we are.  We therefore also check if our confidence interval
        // gives us a potential value range which spans the actual value, and if it does we
        // fail it without even running the test.
        boolean seenLower = false;
        boolean seenHigher = false;
        for (int m = Math.max((int) Math.floor(ci.getLowerBound() * 100), 0); m <= Math.min((int) Math.ceil(ci.getUpperBound() * 100), 100); m++) {
            double expectedPercent = expectedEnds[m];
            double diff = expectedPercent - toPercent;
            if (diff <= 0)
                seenLower = true;
            if (diff >= 0)
                seenHigher = true;
            if (Math.abs(diff) < smallestTheoreticalToActualDiff) {
                worseCaseExpectedPercent = expectedPercent;
                smallestTheoreticalToActualDiff = Math.abs(diff);
            }
        }
        // Sanity check
        if (smallestTheoreticalToActualDiff > Math.abs((toPercent - expectedEnds[Math.round(fromPercent)]))) {
            throw new IllegalStateException("Can't have a worst case which is better than the actual");
        }
        if (Math.abs(toPercent - worseCaseExpectedPercent) < minPercentShift)
            continue;
        // If they want to use the current quantitation as well then we can do that calculation now.
        if (useCurrentQuant) {
            try {
                if (Math.abs(toStore.getValueForProbe(probes[p]) - expectedEnds[Math.round(fromStore.getValueForProbe(probes[p]))]) < minPercentShift)
                    continue;
            } catch (SeqMonkException sme) {
                throw new IllegalStateException(sme);
            }
        }
        // Check the directionality
        if (aboveOnly && worseCaseExpectedPercent - toPercent > 0)
            continue;
        if (belowOnly && worseCaseExpectedPercent - toPercent < 0)
            continue;
        // Now perform the Binomial test.
        double pValue = bt.binomialTest(forCount + revCount, forCount, worseCaseExpectedPercent / 100d, hypothesis);
        // Our confidence range spanned the actual value we had so we can't be significant
        if (seenLower && seenHigher)
            pValue = 0.5;
        // System.err.println("P value is "+pValue);
        // Store this as a potential hit (after correcting p-values later)
        hits.add(new ProbeTTestValue(probes[p], pValue));
    }
    // Now we can correct the p-values if we need to
    ProbeTTestValue[] rawHits = hits.toArray(new ProbeTTestValue[0]);
    if (applyMultipleTestingCorrection) {
        // System.err.println("Correcting for "+rawHits.length+" tests");
        BenjHochFDR.calculateQValues(rawHits);
    }
    for (int h = 0; h < rawHits.length; h++) {
        if (applyMultipleTestingCorrection) {
            if (rawHits[h].q < stringency) {
                newList.addProbe(rawHits[h].probe, (float) rawHits[h].q);
            }
        } else {
            if (rawHits[h].p < stringency) {
                newList.addProbe(rawHits[h].probe, (float) rawHits[h].p);
            }
        }
    }
    filterFinished(newList);
}

Example 69 with ProbeList

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList in project SeqMonk by s-andrews.

the class ChiSquareFilter method generateProbeList.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Filters.ProbeFilter#generateProbeList()
	 */
protected void generateProbeList() {
    if (options.stringencyField.getText().length() == 0) {
        stringency = 0.05;
    } else {
        stringency = Double.parseDouble(options.stringencyField.getText());
    }
    if (options.minObservationsField.getText().length() == 0) {
        minObservations = 10;
    } else {
        minObservations = Integer.parseInt(options.minObservationsField.getText());
    }
    if (options.minDifferenceField.getText().length() == 0) {
        minPercentShift = 10;
    } else {
        minPercentShift = Integer.parseInt(options.minDifferenceField.getText());
    }
    applyMultipleTestingCorrection = options.multiTestBox.isSelected();
    pairs = options.getSelectedPairs();
    ProbeList newList;
    if (applyMultipleTestingCorrection) {
        newList = new ProbeList(startingList, "Filtered Probes", "", "Q-value");
    } else {
        newList = new ProbeList(startingList, "Filtered Probes", "", "P-value");
    }
    Probe[] probes = startingList.getAllProbes();
    int[][] pairCounts = new int[pairs.length][2];
    // This is where we'll store any hits
    Vector<ProbeTTestValue> hits = new Vector<ProbeTTestValue>();
    PROBE: for (int p = 0; p < probes.length; p++) {
        if (p % 100 == 0) {
            progressUpdated("Processed " + p + " probes", p, probes.length);
        }
        if (cancel) {
            cancel = false;
            progressCancelled();
            return;
        }
        // For each dataset make up a list of forward and reverse probes under this probe
        for (int d = 0; d < pairs.length; d++) {
            pairCounts[d][0] = pairs[d].store1.getReadsForProbe(probes[p]).length;
            pairCounts[d][1] = pairs[d].store2.getReadsForProbe(probes[p]).length;
        }
        // See if we have enough counts and difference to go on with this
        double minPercent = 0;
        double maxPercent = 0;
        for (int d = 0; d < pairs.length; d++) {
            if (pairCounts[d][0] + pairCounts[d][1] < minObservations) {
                continue PROBE;
            }
            double percent = (((double) pairCounts[d][0]) / (pairCounts[d][0] + pairCounts[d][1])) * 100;
            if (d == 0 || percent < minPercent)
                minPercent = percent;
            if (d == 0 || percent > maxPercent)
                maxPercent = percent;
        }
        if (maxPercent - minPercent < minPercentShift)
            continue PROBE;
        // Now perform the Chi-Square test.
        double pValue = ChiSquareTest.chiSquarePvalue(pairCounts);
        // Store this as a potential hit (after correcting p-values later)
        hits.add(new ProbeTTestValue(probes[p], pValue));
    }
    // Now we can correct the p-values if we need to
    ProbeTTestValue[] rawHits = hits.toArray(new ProbeTTestValue[0]);
    if (applyMultipleTestingCorrection) {
        BenjHochFDR.calculateQValues(rawHits);
    }
    for (int h = 0; h < rawHits.length; h++) {
        if (applyMultipleTestingCorrection) {
            if (rawHits[h].q < stringency) {
                newList.addProbe(rawHits[h].probe, (float) rawHits[h].q);
            }
        } else {
            if (rawHits[h].p < stringency) {
                newList.addProbe(rawHits[h].probe, (float) rawHits[h].p);
            }
        }
    }
    filterFinished(newList);
}

Example 70 with ProbeList

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList in project SeqMonk by s-andrews.

the class ChiSquareFilterForRev method generateProbeList.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Filters.ProbeFilter#generateProbeList()
	 */
protected void generateProbeList() {
    if (options.stringencyField.getText().length() == 0) {
        stringency = 0.05;
    } else {
        stringency = Double.parseDouble(options.stringencyField.getText());
    }
    if (options.minObservationsField.getText().length() == 0) {
        minObservations = 10;
    } else {
        minObservations = Integer.parseInt(options.minObservationsField.getText());
    }
    if (options.minDifferenceField.getText().length() == 0) {
        minPercentShift = 10;
    } else {
        minPercentShift = Integer.parseInt(options.minDifferenceField.getText());
    }
    applyMultipleTestingCorrection = options.multiTestBox.isSelected();
    resample = options.resampleBox.isSelected();
    Probe[] probes = startingList.getAllProbes();
    if (resample) {
        // Do a sanity check that the current quantitation actually looks like
        // percentage values.
        progressUpdated("Checking current quantitations", 0, 1);
        for (int p = 0; p < probes.length; p++) {
            if (cancel) {
                progressCancelled();
                return;
            }
            try {
                for (int d = 0; d < stores.length; d++) {
                    float value = stores[d].getValueForProbe(probes[p]);
                    // NaN is OK
                    if (Float.isNaN(value))
                        continue;
                    if (value < 0 || value > 100) {
                        progressExceptionReceived(new SeqMonkException("For resampling quantitations must be between 0 and 100.  Probe " + probes[p].name() + " had value " + value + " in " + stores[d].name()));
                        return;
                    }
                }
            } catch (SeqMonkException sme) {
                progressExceptionReceived(sme);
                return;
            }
        }
    }
    ProbeList newList;
    if (applyMultipleTestingCorrection) {
        newList = new ProbeList(startingList, "Filtered Probes", "", "Q-value");
    } else {
        newList = new ProbeList(startingList, "Filtered Probes", "", "P-value");
    }
    int[][] forRevCounts = new int[stores.length][2];
    // This is where we'll store any hits
    Vector<ProbeTTestValue> hits = new Vector<ProbeTTestValue>();
    PROBE: for (int p = 0; p < probes.length; p++) {
        if (p % 100 == 0) {
            progressUpdated("Processed " + p + " probes", p, probes.length);
        }
        if (cancel) {
            cancel = false;
            progressCancelled();
            return;
        }
        // For each dataset make up a list of forward and reverse probes under this probe
        for (int d = 0; d < stores.length; d++) {
            long[] reads = stores[d].getReadsForProbe(probes[p]);
            forRevCounts[d][0] = 0;
            forRevCounts[d][1] = 0;
            if (resample) {
                try {
                    float value = stores[d].getValueForProbe(probes[p]);
                    // We redistribute the total count based on the percentage value
                    // in the quantitation
                    int methCount = Math.round((reads.length * value) / 100);
                    int unmethCount = reads.length - methCount;
                    forRevCounts[d][0] = methCount;
                    forRevCounts[d][1] = unmethCount;
                } catch (SeqMonkException sme) {
                    continue PROBE;
                }
            } else {
                for (int r = 0; r < reads.length; r++) {
                    if (SequenceRead.strand(reads[r]) == Location.FORWARD) {
                        ++forRevCounts[d][0];
                    } else if (SequenceRead.strand(reads[r]) == Location.REVERSE) {
                        ++forRevCounts[d][1];
                    }
                }
            }
        }
        // See if we have enough counts and difference to go on with this
        double minPercent = 0;
        double maxPercent = 0;
        for (int d = 0; d < stores.length; d++) {
            if (forRevCounts[d][0] + forRevCounts[d][1] < minObservations) {
                continue PROBE;
            }
            double percent = (((double) forRevCounts[d][0]) / (forRevCounts[d][0] + forRevCounts[d][1])) * 100;
            if (d == 0 || percent < minPercent)
                minPercent = percent;
            if (d == 0 || percent > maxPercent)
                maxPercent = percent;
        }
        if (maxPercent - minPercent < minPercentShift)
            continue PROBE;
        // Now perform the Chi-Square test.
        double pValue = ChiSquareTest.chiSquarePvalue(forRevCounts);
        // Store this as a potential hit (after correcting p-values later)
        hits.add(new ProbeTTestValue(probes[p], pValue));
    }
    // Now we can correct the p-values if we need to
    ProbeTTestValue[] rawHits = hits.toArray(new ProbeTTestValue[0]);
    if (applyMultipleTestingCorrection) {
        BenjHochFDR.calculateQValues(rawHits);
    }
    for (int h = 0; h < rawHits.length; h++) {
        if (applyMultipleTestingCorrection) {
            if (rawHits[h].q < stringency) {
                newList.addProbe(rawHits[h].probe, (float) rawHits[h].q);
            }
        } else {
            if (rawHits[h].p < stringency) {
                newList.addProbe(rawHits[h].probe, (float) rawHits[h].p);
            }
        }
    }
    filterFinished(newList);
}