public List<String> find() throws IOException {
// Set<String> g1 = new HashSet<String>(Arrays.asList("HRAS", "NRAS", "KRAS"));
// Set<String> g2 = new HashSet<String>(Arrays.asList("BRAF"));
Set<String> g1 = new HashSet<String>(Arrays.asList("HRAS"));
Set<String> g2 = new HashSet<String>(Arrays.asList("NRAS", "KRAS"));
Map<String, Double> pvals = calcDifferencePvals(g1, g2);
System.out.println("pvals.size() = " + pvals.size());
List<String> list = FDR.select(pvals, null, fdrThr);
System.out.println("result size = " + list.size());
Map<String, Boolean> dirs = getChangeDirections(list, g1, g2);
int up = 0;
int dw = 0;
for (String gene : dirs.keySet()) {
Boolean d = dirs.get(gene);
if (d) up++;
else dw++;
}
System.out.println("up = " + up);
System.out.println("dw = " + dw);
return list;
}
private double[] toDoubleArray(Map<String, Double> map) {
double[] d = new double[map.size()];
int i = 0;
for (String key : map.keySet()) {
d[i++] = map.get(key);
}
return d;
}
public Map<String, Boolean> getChangeDirections(
List<String> genes, Set<String> g1, Set<String> g2) {
boolean[][] b = getExclusiveMutations(g1, g2);
Map<String, Boolean> dirs = new HashMap<String, Boolean>();
for (String gene : genes) {
dirs.put(gene, getChangeDirection(gene, b[0], b[1]));
}
return dirs;
}
private void printResults(Map<String, Double> pvals, List<String> list) {
for (String s : list) {
System.out.println(
s
+ "\t"
+ FormatUtil.roundToSignificantDigits(pvals.get(s), 2)
+ "\t"
+ affectedDw.get(s));
}
}
private Map<String, Double> getExpressionPvals(
Set<String> targets, boolean[] set1, boolean[] set2) {
Map<String, Double> map = new HashMap<String, Double>();
Histogram2D h = new Histogram2D(0.2);
System.out.println("targets = " + targets.size());
Progress prg = new Progress(targets.size());
for (String sym : targets) {
prg.tick();
if (expMan.getNonZeroRatio(sym) == 0) continue;
double pval = calcDiffPval(sym, set1, set2, true);
if (Double.isNaN(pval)) continue;
if (pval == 0) pval = 1E-11;
double pPerm = calcDiffPval(sym, set1, set2, false);
if (pPerm == 0) pPerm = 1E-5;
h.count(-Math.log(pval), -Math.log(pPerm));
// pval = 0 is not real and it is not compatible with fisher's combined probability.
// below is a better approximation.
// if (pval == 0)
// {
// pval = 1E-11;
// }
map.put(sym, pval);
}
Histogram2DPlot p = new Histogram2DPlot(h);
p.setLines(Arrays.asList(new double[] {1, 0}));
p.setVisible(true);
return map;
}
