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;
}
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));
}
}