private Set<String> getDownstream(String mut) {
Set<String> tfs = new HashSet<String>();
tfs.add(mut);
if (depth > 1) tfs.addAll(travSt.getDownstream(tfs, depth - 1));
return travExp.getDownstream(tfs);
}
public static void main(String[] args) throws IOException {
Graph graphSt;
Graph graphExp;
GiovannisAnalysis finder;
Dataset1 dataset = Dataset1.THCA;
int depth = 3;
double fdrThr = 0.01;
graphSt = PathwayCommons.getGraph(SIFEnum.CONTROLS_STATE_CHANGE_OF);
graphExp = PathwayCommons.getGraph(SIFEnum.CONTROLS_EXPRESSION_OF);
graphExp.merge(MSigDBTFT.getGraph());
finder = new GiovannisAnalysis(graphSt, graphExp, dataset, depth, fdrThr);
checkZeros(finder.expMan);
finder.find();
}
private void writeSelf(
String origTarget, GeneBranch currentParent, GeneBranch down, Writer writer1, Writer writer2)
throws IOException {
if (!down.isSelected()) return;
String edgeTag;
if (down.isLeaf() || travExp.getUpstream(down.gene).contains(currentParent)) {
edgeTag = SIFEnum.CONTROLS_EXPRESSION_OF.getTag();
} else edgeTag = SIFEnum.CONTROLS_STATE_CHANGE_OF.getTag();
writer1.write(currentParent.gene + "\t" + edgeTag + "\t" + down.gene + "\n");
writeWeights(origTarget, currentParent, down, edgeTag, writer2);
writeBranches(origTarget, down, writer1, writer2);
}