Examples with AlternativeHypothesis org.apache.commons.math3.stat.inference.AlternativeHypothesis used on opensource projects

Example 1 with AlternativeHypothesis

use of org.apache.commons.math3.stat.inference.AlternativeHypothesis 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);
}