Method fillInRatio

src/GenomeCopyNumber.cpp:1284–1310

}

int GenomeCopyNumber::fillInRatio() {
    vector <float> countValues;
    vector<ChrCopyNumber>::iterator it;

    for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) {
        if ((sex_.compare("XY")==0) && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) {
                //should take into account that normally one has only one copy of X and Y..
                it->fillInRatio(isRatioLogged_);
        } else {
                it->fillInRatio(isRatioLogged_);
                for (int i = 0; i< it->getLength(); i++) {
                    if (it->getValueAt(i)>0) {
                        countValues.push_back(it->getRatioAtBin(i));
                    }
                }
        }
    }
    float median=get_medianNotNA(countValues);
    for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) {
        if (!isRatioLogged_) {
                it->recalculateRatio(median);
        } else {
            it->recalculateLogRatio(median);
        }
    }
    return 1;
}

int GenomeCopyNumber::calculateRatio( GenomeCopyNumber & controlCopyNumber, int degree, bool intercept) {