bool NeighborClustCount(Neighbor** vNeighbors,vector<int>& vClustIDs,vector<ClusterInfo>& vPrct,int iNNToFind,int iClusts)
{
int iSz = vClustIDs.size();
if(vPrct.size()!=iClusts+1)
return false;
int i;
vector<int> vCounts(iClusts+1);
for(i=1;i<=iClusts;i++)
vCounts[i]=count(vClustIDs.begin(),vClustIDs.end(),i);
vector< vector<prob_t> > vprct(iClusts+1);
for(i=1;i<=iClusts;i++)
vprct[i]=vector<prob_t>(vCounts[i],0.0);
vector<int> vIndex(iClusts+1,0);
for(i=0;i<iSz;i++)
{
int j, iCount = 0, iClust = vClustIDs[i];
if(!iClust)continue;//skip background vectors
int idx = vIndex[iClust]++;
for(j=0;j<iNNToFind;j++)
{
if(vClustIDs[vNeighbors[i][j].m_id]==iClust)
vprct[iClust][idx]+=1.0f;
}
vprct[iClust][idx] /= iNNToFind;
}
for(i=1;i<=iClusts;i++)
vPrct[i].m_fPrctKNNInClust=Avg(vprct[i]);
return true;
}
void CNProbeSetArray::setupGCCorrectionBins(int iGCBinCount)
{
AffxMultiDimensionalArray<float> vGcContent(getProcessCount());
int iIndex = 0;
for (int iRowIndex = 0; (iRowIndex < getCount()); iRowIndex++) {
CNProbeSet* p = getAt(iRowIndex);
if (!p->isProcess() || !( p->processAsCN() || p->processAsSNP() )) {
continue;
}
float fGcContent = p->getGCContent();
vGcContent.set(iIndex, fGcContent);
iIndex++;
}
AffxMultiDimensionalArray<float> v(iGCBinCount);
AffxMultiDimensionalArray<int> vCounts(iGCBinCount);
float fPercentile = 0;
for (int iBinIndex = 0; (iBinIndex < iGCBinCount); iBinIndex++) {
fPercentile = vGcContent.percentile((1.0 / (double)iGCBinCount) * (iBinIndex + 1));
v.set(iBinIndex, fPercentile);
}
v.set((iGCBinCount - 1), 1);
for (int iRowIndex = 0; (iRowIndex < getCount()); iRowIndex++) {
CNProbeSet* pobjProbeSet = getAt(iRowIndex);
if (!pobjProbeSet->isProcess() || !( pobjProbeSet->processAsCN() || pobjProbeSet->processAsSNP() )) {
continue;
}
float fGcContent = pobjProbeSet->getGCContent();
for (int iBinIndex = 0; (iBinIndex < iGCBinCount); iBinIndex++) {
if (fGcContent <= v.get(iBinIndex)) {
if (iBinIndex == 0) {
pobjProbeSet->setGCBinIndex(iBinIndex);
vCounts.increment(iBinIndex);
break;
} else if (fGcContent > v.get(iBinIndex - 1)) {
pobjProbeSet->setGCBinIndex(iBinIndex);
vCounts.increment(iBinIndex);
break;
}
}
}
if (pobjProbeSet->getGCBinIndex() == -1) {
Verbose::out(1, pobjProbeSet->getProbeSetName() + " has no gc-bin assignment. " + ::getDouble(fGcContent, 6));
}
}
/*
Verbose::out(1, "*");
AffxString str;
for (int iBinIndex = 0; (iBinIndex < iGCBinCount); iBinIndex++)
{
if (iBinIndex == 0)
{
Verbose::out(1, str + "GC Correction Bin " + ::getInt(iBinIndex + 1) + "\t= 0 \t<= n <= " + ::getDouble(v.get(iBinIndex), 6) + "\tMarkerCount = " + ::getInt(vCounts.get(iBinIndex)));
}
else if (iBinIndex == (iGCBinCount - 1))
{
Verbose::out(1, str + "GC Correction Bin " + ::getInt(iBinIndex + 1) + "\t= " + ::getDouble(v.get(iBinIndex - 1), 6) + "\t< n <= 1 \tMarkerCount = " + ::getInt(vCounts.get(iBinIndex)));
}
else
{
Verbose::out(1, str + "GC Correction Bin " + ::getInt(iBinIndex + 1) + "\t= " + ::getDouble(v.get(iBinIndex - 1), 6) + "\t< n <= " + ::getDouble(v.get(iBinIndex), 6) + "\tMarkerCount = " + ::getInt(vCounts.get(iBinIndex)));
}
}
Verbose::out(1, "*");
*/
}
