public static ClassCharacteristicSetKmer<A> BuildSubtractiveDifference(string name, MultisetKmer<A> baselineClass, MultisetKmer<A> thisClass, uint countCutoff)
{
ClassCharacteristicSetKmer<A> newSet = new ClassCharacteristicSetKmer<A>(name, Math.Min (baselineClass.maxK, thisClass.maxK));
//TODO statistically significant?
//TODO diffence amount?
foreach(Kmer<A> key in thisClass.Keys){
if(thisClass.getCount(key) > countCutoff){
double thisFrac = thisClass.GetKeyFrac(key);
double baseFrac = baselineClass.GetKeyFrac (key);
if(thisFrac > baseFrac){
newSet.Add (key, thisFrac - baseFrac);
}
}
}
//TODO select top x?
//double[] function?
return newSet;
}
public void TrainModelRatios(MultisetKmer <A> baselineClass, MultisetKmer <A> thisClass)
{
List <KeyValuePair <Kmer <A>, double> > rawModel = new List <KeyValuePair <Kmer <A>, double> >();
int totalCount = 0;
foreach (Kmer <A> key in thisClass.Keys)
{
int thisCount = thisClass.getCount(key);
totalCount += thisCount;
if (thisCount > regressor.minSignificantCount)
{
double thisFrac = thisClass.GetKeyFrac(key);
double baseFrac = baselineClass.GetKeyFracLaplace(key, regressor.smoothingAmount);
if (thisFrac > baseFrac)
{
rawModel.Add(key, thisFrac / baseFrac);
}
}
}
regressor.finalizeModel(rawModel, totalCount);
}