public void CaseControlEvaluation(GeneticDistance newGeneticDistance, MapData newMapData, BlockDictionary newBlockDictionary, Commands newCommands, ResultList finalResultList)
{
SnpDataSet caseData = new SnpDataSet(); //Creat Case data set
SnpDataSet controlData = new SnpDataSet(); //Creat Control data set
Console.Write("\tReading ped data...");
Inputdata inputData = new Inputdata();
inputData.data(caseData, controlData, newCommands); //start getting the data and put into case/comtrol set
ArrayList controlIndividualList = new ArrayList();
ArrayList caseIndividualList = new ArrayList();
Console.Write("finished.\n");
inputData = null;
GC.Collect();
Console.Write("Analyzing LD data...");
double[,] controlLinkageData = new double[controlData.GetSnpCount(), 7];
//caseData.Linkage(caseLinkageData);
controlData.SetIndividualList(controlIndividualList);
controlData = null;
GC.Collect();
Console.Write("finished.\n");
finalResultList.SetControlResult(caseData.individual.Length, 0.2);
Console.WriteLine("Haplotyping for all the control samples...");
for (int indIndex = 0; indIndex < controlIndividualList.Count; indIndex++)
{
((Individual)(controlIndividualList[indIndex])).SetIndividualID(indIndex);
}
int ind = 0;
foreach (Individual newIndividual in controlIndividualList) //haplotyping for each individual.
{
newIndividual.Haplotyping(newBlockDictionary, newMapData, controlLinkageData);
ind++;
Console.SetCursorPosition(8, Console.CursorTop);
Console.Write("{0} / {1}", ind, controlIndividualList.Count);
}
Console.Write("\t\tFinished.\n");
for (int n = 0; n < newCommands.permutation; n++) //permutation
{
Console.Write("Iteration: {0} / {1} \n", n + 1, newCommands.permutation);
List <GroupShare> resultList = new List <GroupShare>(); //unfinished result from last window
List <int> selectControlList = new List <int>();
selectControlList = this.Select(controlIndividualList.Count, caseData.individual.Length, new Random());
//selectControlList = this.Select(controlIndividualList.Count, 30, new Random());
for (int windowStart = 0; windowStart <= newBlockDictionary.blockList.Count - 1; windowStart += 30000)
{
List <GroupShare> newResultList = new List <GroupShare>();
int windowEnd = Math.Min(windowStart + 30000, newBlockDictionary.blockList.Count - 1);
ArrayList wholePairwiseIBDRegionList = new ArrayList();
Console.WriteLine("\t\tSearching for pairwise sharing regions");
for (int i = 0; i < selectControlList.Count; i++)
{
for (int j = i + 1; j < selectControlList.Count; j++)
{
((Individual)controlIndividualList[selectControlList[i]]).PairwiseComparison(wholePairwiseIBDRegionList, (Individual)controlIndividualList[selectControlList[j]], (Block[])newBlockDictionary.blockList.ToArray(typeof(Block)), newMapData, newCommands.cut, windowStart, windowEnd);
}
Console.SetCursorPosition(16, Console.CursorTop);
Console.Write("{0} / {1}\tTotal regions: {2}", i + 1, selectControlList.Count, wholePairwiseIBDRegionList.Count);
}
Console.WriteLine("\t\tFinished.");
MyIBDComparer newComparer = new MyIBDComparer();
wholePairwiseIBDRegionList.Sort(newComparer);
GroupShareFinder newIBDList = new GroupShareFinder(wholePairwiseIBDRegionList);
Console.WriteLine("\t\tSrart searching for group sharing regions: ");
newIBDList.findGroupIBD(controlIndividualList, newBlockDictionary, controlLinkageData, newResultList, resultList, windowStart, windowEnd);
finalResultList.AddNewControlList(newResultList, caseData.individual.Length, 0.2);
}
}
Console.WriteLine("Finished permutation in controls");
finalResultList.CalculateControlResultParameters();
Console.WriteLine("Finished puermutation result calculation");
caseData.SetIndividualList(caseIndividualList);
caseData = null;
GC.Collect();
Console.WriteLine("Haplotyping for all case samples...");
for (int indIndex = 0; indIndex < caseIndividualList.Count; indIndex++)
{
((Individual)(caseIndividualList[indIndex])).SetIndividualID(indIndex);
}
ind = 0;
foreach (Individual newIndividual in caseIndividualList) //haplotyping for each individual.
{
newIndividual.Haplotyping(newBlockDictionary, newMapData, controlLinkageData);
ind++;
Console.SetCursorPosition(8, Console.CursorTop);
Console.Write("{0} / {1}", ind, caseIndividualList.Count);
}
Console.Write("\t\tFinished.\n");
for (int n = 0; n < 1; n++) //case evaluation
{
Console.Write("\tTotally {0} blocks will be analyzed.\n", newBlockDictionary.blockList.Count);
List <GroupShare> resultList = new List <GroupShare>(); //unfinished result from last window
for (int windowStart = 0; windowStart <= newBlockDictionary.blockList.Count - 1; windowStart += 30000)
{
List <GroupShare> newResultList = new List <GroupShare>();
int windowEnd = Math.Min(windowStart + 30000, newBlockDictionary.blockList.Count - 1);
Console.WriteLine("\tAnalyzing block {0} to {1}", windowStart, windowEnd - 1);
ArrayList wholePairwiseIBDRegionList = new ArrayList();
Console.WriteLine("\t\tSearching for pairwise sharing regions");
for (int i = 0; i < caseIndividualList.Count; i++)
{
for (int j = i + 1; j < caseIndividualList.Count; j++)
{
((Individual)caseIndividualList[i]).PairwiseComparison(wholePairwiseIBDRegionList, (Individual)caseIndividualList[j], (Block[])newBlockDictionary.blockList.ToArray(typeof(Block)), newMapData, newCommands.cut, windowStart, windowEnd);
}
Console.SetCursorPosition(16, Console.CursorTop);
Console.Write("{0} / {1}\tTotal regions: {2}", i + 1, caseIndividualList.Count, wholePairwiseIBDRegionList.Count);
}
Console.WriteLine("\n\t\tFinished searching pairwise sharing regions");
MyIBDComparer newComparer = new MyIBDComparer();
wholePairwiseIBDRegionList.Sort(newComparer);
GroupShareFinder newIBDList = new GroupShareFinder(wholePairwiseIBDRegionList);
Console.WriteLine("\t\tSrart searching for group sharing regions:");
newIBDList.findGroupIBD(caseIndividualList, newBlockDictionary, controlLinkageData, newResultList, resultList, windowStart, windowEnd);
finalResultList.calculateAllPvalue(newResultList, caseIndividualList.Count, 0.2, newCommands);
finalResultList.Combine(newResultList);
finalResultList.ClearReplication();
}
}
finalResultList.PrintResult(newBlockDictionary, caseIndividualList.Count, 0.2, newCommands);
}
public void PairwiseComparison(ArrayList pairwiseIBDRegionList, Individual thatIndividual, Block[] blockList, MapData newMapData, double lengthCut, int startBlockID, int endBlockID)
{
PairwiseIBDRegion newPairwiseIBDRegion = new PairwiseIBDRegion(this.GetIndividualID(), thatIndividual.GetIndividualID(), 0, 0, -1, -1);
for (int blockID = startBlockID; blockID < endBlockID; blockID++) //foreach block, from first to end.
{
if (newPairwiseIBDRegion.GetLastBlockID() == -1) // last IBD region has just added or deleted, need to construc a new one.
{
newPairwiseIBDRegion.SetStart(blockList[blockID].GetStartSnpID());
newPairwiseIBDRegion.SetEnd(blockList[blockID].GetEndSnpID());
newPairwiseIBDRegion.SetLastBlockID(blockID);
newPairwiseIBDRegion.SetFirstBlockID(blockID);
newPairwiseIBDRegion.ClearHaplotype();
}
ArrayList sharedHaplotypeID = new ArrayList();
ArrayList thisHaplotypeList = new ArrayList(); //store all the possible haplotype for this individual in this block.
ArrayList thatHaplotypeList = new ArrayList(); //store all the possible haplotype for that individual in this block.
bool thisUnknownHaplotype = false;
bool thatUnknownHaplotype = false;
for (int i = 0; i < this.haplotype[blockID].Count; i++) //store all the possible haplotype for this individual in this block.
{
if (((HaplotypePair)this.haplotype[blockID][i]).firstHaplotypeID != -1)
{
thisHaplotypeList.Add(((HaplotypePair)this.haplotype[blockID][i]).firstHaplotypeID);
}
else
{
thisUnknownHaplotype = true;
break;
}
if (((HaplotypePair)this.haplotype[blockID][i]).secondHaplotypeID != -1 && ((HaplotypePair)this.haplotype[blockID][i]).secondHaplotypeID != ((HaplotypePair)this.haplotype[blockID][i]).firstHaplotypeID)
{
thisHaplotypeList.Add(((HaplotypePair)this.haplotype[blockID][i]).secondHaplotypeID);
}
else
{
if (((HaplotypePair)this.haplotype[blockID][i]).secondHaplotypeID == -1)
{
thisUnknownHaplotype = true;
}
break;
}
}
for (int i = 0; i < thatIndividual.haplotype[blockID].Count; i++)//store all the possible haplotype for that individual in this block.
{
if (((HaplotypePair)thatIndividual.haplotype[blockID][i]).firstHaplotypeID != -1)
{
thatHaplotypeList.Add(((HaplotypePair)thatIndividual.haplotype[blockID][i]).firstHaplotypeID);
}
else
{
thatUnknownHaplotype = true;
break;
}
if (((HaplotypePair)thatIndividual.haplotype[blockID][i]).secondHaplotypeID != -1 && ((HaplotypePair)thatIndividual.haplotype[blockID][i]).secondHaplotypeID != ((HaplotypePair)thatIndividual.haplotype[blockID][i]).firstHaplotypeID)
{
thatHaplotypeList.Add(((HaplotypePair)thatIndividual.haplotype[blockID][i]).secondHaplotypeID);
}
else
{
if (((HaplotypePair)thatIndividual.haplotype[blockID][i]).secondHaplotypeID == -1)
{
thatUnknownHaplotype = true;
}
break;
}
}
if (thisUnknownHaplotype && thatUnknownHaplotype) //found unknown haplotype in both sample
{
for (int s = 0; s < blockList[blockID].GetHaplotypeCount(); s++)
{
sharedHaplotypeID.Add(s);
}
}
else if (thisUnknownHaplotype && !thatUnknownHaplotype) // only in this sample
{
foreach (int newId in thatHaplotypeList)
{
sharedHaplotypeID.Add(newId);
}
}
else if ((!thisUnknownHaplotype) && thatUnknownHaplotype) // only that sample
{
foreach (int newId in thisHaplotypeList)
{
sharedHaplotypeID.Add(newId);
}
}
else // normal case ,non unknown
{
thisHaplotypeList.Sort();
thatHaplotypeList.Sort();
int thisHaplotypeIndex = 0;
int thatHaplotypeIndex = 0;
while (thisHaplotypeIndex < thisHaplotypeList.Count && thatHaplotypeIndex < thatHaplotypeList.Count)
{ // store all the shared haplotype id in the sharedHaplotypeID list.
if ((int)thisHaplotypeList[thisHaplotypeIndex] == (int)thatHaplotypeList[thatHaplotypeIndex])
{
sharedHaplotypeID.Add(thisHaplotypeList[thisHaplotypeIndex]);
thisHaplotypeIndex++;
thatHaplotypeIndex++;
}
else if ((int)thisHaplotypeList[thisHaplotypeIndex] < (int)thatHaplotypeList[thatHaplotypeIndex])
{
thisHaplotypeIndex++;
}
else
{
thatHaplotypeIndex++;
}
}
}
bool shareRecombinationRegion = true;
if (sharedHaplotypeID.Count == 0) // no shared haplotype found!
{
if (newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetEnd()) - newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetStart()) >= lengthCut / 10) // only add the pairwise IBD region whose length is >= 2cm
{
if (newPairwiseIBDRegion.GetLastBlockID() - newPairwiseIBDRegion.GetFirstBlockID() != 0)
{
if (pairwiseIBDRegionList.Count == 0 || !this.CombineAdjacentPairwiseRegion((PairwiseIBDRegion)pairwiseIBDRegionList[pairwiseIBDRegionList.Count - 1], newPairwiseIBDRegion, thatIndividual))
{
if (newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetEnd()) - newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetStart()) >= lengthCut)
{
pairwiseIBDRegionList.Add(newPairwiseIBDRegion.GetCopy());
}
}
}
}
newPairwiseIBDRegion.SetLastBlockID(-1);
continue;
}
else
{
newPairwiseIBDRegion.SetEnd(blockList[blockID].GetEndSnpID());
newPairwiseIBDRegion.AddHaplotype(sharedHaplotypeID);
newPairwiseIBDRegion.SetLastBlockID(blockID);
if (blockID == blockList.Length - 1)
{
if (newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetEnd()) - newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetStart()) >= lengthCut)
{
if (pairwiseIBDRegionList.Count == 0 || !this.CombineAdjacentPairwiseRegion((PairwiseIBDRegion)pairwiseIBDRegionList[pairwiseIBDRegionList.Count - 1], newPairwiseIBDRegion, thatIndividual))
{
if (newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetEnd()) - newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetStart()) >= lengthCut)
{
pairwiseIBDRegionList.Add(newPairwiseIBDRegion.GetCopy());
}
}
}
return;
}
else
{
for (int i = blockList[blockID].GetEndSnpID() + 1; i < blockList[blockID + 1].GetStartSnpID(); i++)
{
if (Math.Abs(this.genotype[i] - thatIndividual.genotype[i]) == 2)
{
if (newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetEnd()) - newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetStart()) >= lengthCut) // only add the pairwise IBD region whose length is >= 2cm
{
if (pairwiseIBDRegionList.Count == 0 || !this.CombineAdjacentPairwiseRegion((PairwiseIBDRegion)pairwiseIBDRegionList[pairwiseIBDRegionList.Count - 1], newPairwiseIBDRegion, thatIndividual))
{
if (newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetEnd()) - newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetStart()) >= lengthCut)
{
pairwiseIBDRegionList.Add(newPairwiseIBDRegion.GetCopy());
}
}
}
newPairwiseIBDRegion.SetLastBlockID(-1);
newPairwiseIBDRegion.SetEnd(i - 1);
break;
}
}
}
}
}
}
