Method calculateXiSum

src/GenomeCopyNumber.cpp:3242–3264

}

double GenomeCopyNumber::calculateXiSum(int ploidy) {
	int totalNumberOfBP = 0;
	double totalSum = 0;
	map <float,float> sds;
	//map <float,float> meds;
	//float varZero = calculateVarianceForNormalCopy(ploidy);
	//calculateSDAndMed(ploidy,sds,meds);
	calculateSDs(ploidy,sds);
	vector<ChrCopyNumber>::iterator it;
	cout << "..Calculating sum of squares for ploidy = "<<ploidy<<"\n";
	for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) {
		//cout << "..processing chromosome " <<it->getChromosome()<<"\n";
		totalNumberOfBP += it->getNumberOfGoodFragments();
		//totalSum += it->getXiSum(ploidy,sqrt(varZero));
		//totalSum += it->calculateXiSum(ploidy,sds,meds);
		totalSum += it->calculateXiSum(ploidy,sds);
	}
	sds.clear();
	//meds.clear();
	cout << "ploidy\t" << ploidy << "\ttest-value\t"<<totalSum<<"\n";
	cout << "ploidy\t" << totalNumberOfBP << "\ttest-value\t"<<totalNumberOfBP<<"\n";
	return totalSum/totalNumberOfBP+15*ploidy;
}

void GenomeCopyNumber::calculateSDAndMed(int ploidy, map <float,float> &sds,map <float,float> &meds) {