Method Percentage_GenomeExplained

src/GenomeCopyNumber.cpp:4355–4386

}

double GenomeCopyNumber::Percentage_GenomeExplained(int & unexplainedChromosomes)
{
	vector<ChrCopyNumber>::iterator it;
	long double fragment_median2 ;
	long double numberOfPoints=0;
	double sum_frags = 0;
	unexplainedChromosomes=0;
    bool unexplained=0;
    int threshold = 10;

	for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) {
		if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) {
			int fragmentLength=0;
			if (unexplained)unexplainedChromosomes++;
            unexplained=0;
            for (int i = 0; i< it->getNumberOfFragments(); i++) { // for each fragment:
                fragment_median2 = it->getMedianValuesAt(i);
                fragmentLength=it->getFragmentLengthsAt(i);
                if (fragmentLength>threshold) {
                    numberOfPoints+=fragmentLength;
                    if (fragment_median2!=NA && abs(fragment_median2-round_by_ploidy(fragment_median2,ploidy_)) >= 1.0/3/ploidy_) {
                        //cout <<  "Unexplained segment: "<<fragment_median2 << "\t";
                            unexplained=1;
                            sum_frags+=fragmentLength;
                    }
                }
            }
        }
	}
	cout << "Total proportion of unexplained regions: "<<sum_frags << " out of " << numberOfPoints<<" = " << sum_frags/numberOfPoints<< endl ;
	return (1-sum_frags/numberOfPoints);
}