private void loadData() throws IOException {
portalAcc = new CBioPortalAccessor(dataset.mutCnCallExpZ);
expMan =
new ExpDataManager(
portalAcc.getGeneticProfileById(dataset.exp.getProfileID()[0]),
portalAcc.getCaseListById(dataset.exp.getCaseListID()));
expMan.setTakeLog(true);
// portalAcc.setCnVerifier(new CNVerifier(expMan, 0.05));
// mutsig = BroadAccessor.getMutsigGenes(dataset.code(), 0.05);
}
private boolean[] getMutated(Set<String> genes) {
boolean[] b = new boolean[portalAcc.getAlterations(genes.iterator().next()).getSize()];
for (String gene : genes) {
AlterationPack alts = portalAcc.getAlterations(gene);
Change[] ch = alts.get(Alteration.MUTATION);
for (int i = 0; i < ch.length; i++) {
if (ch[i].isAltered()) b[i] = true;
}
}
return b;
}
/**
* Gets the samples that the gene is either mutated or intact. In both cases it is expressed, and
* not copy number lost.
*/
private boolean[] selectSubset(String symbol, boolean mutated) {
AlterationPack alts = portalAcc.getAlterations(symbol);
Change[] muts = alts.get(Alteration.MUTATION);
Change[] cncs = alts.get(Alteration.COPY_NUMBER);
Change[] expz = alts.get(Alteration.EXPRESSION);
boolean[] x = new boolean[alts.getSize()];
for (int i = 0; i < x.length; i++) {
if (ADD_CN_TO_MUT) {
x[i] =
(mutated ? muts[i].isAltered() || cncs[i].isAltered() : muts[i] == Change.NO_CHANGE)
&& cncs[i] == Change.NO_CHANGE
&& expz[i] != Change.INHIBITING
&& !expz[i].isAbsent();
} else {
x[i] =
(mutated ? muts[i].isAltered() : muts[i] == Change.NO_CHANGE)
&& cncs[i] != Change.INHIBITING
&& expz[i] != Change.INHIBITING
&& !cncs[i].isAbsent()
&& !expz[i].isAbsent();
}
}
return x;
}
private boolean[] getCopyNumberUnchanged(String symbol) {
AlterationPack alts = portalAcc.getAlterations(symbol);
if (alts == null) return null;
Change[] cnc = alts.get(Alteration.COPY_NUMBER);
if (cnc == null) return null;
boolean[] b = new boolean[cnc.length];
for (int i = 0; i < b.length; i++) {
b[i] = !USE_COPY_NUMBER_UNCHANGED || !cnc[i].isAltered() && !cnc[i].isAbsent();
}
return b;
}
