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hub / github.com/BoevaLab/FREEC / removeLargeExons

Method removeLargeExons

src/GenomeCopyNumber.cpp:4179–4198  ·  view source on GitHub ↗

Source from the content-addressed store, hash-verified

4177 return 0;
4178}
4179float GenomeCopyNumber::removeLargeExons(float iqrToKeep) {
4180 float maxLength = 0;
4181 vector<ChrCopyNumber>::iterator it;
4182 int totalNumberExons=0;
4183 float numberOfRemovedExons = 0;
4184 vector <float> exonLengths;
4185
4186 for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) {
4187 for (int i=0; i < it->getLength(); i++) {
4188 exonLengths.push_back(it->getEndAtBin(i)-it->getCoordinateAtBin(i));
4189 totalNumberExons++;
4190 }
4191 }
4192 maxLength=get_iqr(exonLengths)/2*iqrToKeep+get_median(exonLengths);
4193
4194 for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) {
4195 numberOfRemovedExons+=it->removeLargeExons(maxLength);
4196 }
4197 return numberOfRemovedExons/totalNumberExons;
4198}
4199int GenomeCopyNumber::focusOnCapture (std::string const& captureFile) {
4200 ifstream file (captureFile.c_str());
4201 string line;

Callers

nothing calls this directly

Calls 5

get_iqrFunction · 0.85
get_medianFunction · 0.85
getEndAtBinMethod · 0.80
getCoordinateAtBinMethod · 0.80
getLengthMethod · 0.45

Tested by

no test coverage detected