public void CalComGroup(Inputdata x)
{
Dx = new double[x.controlData.GetUpperBound(1), x.controlData.GetUpperBound(1)];
double[,] linkageData = new double[x.Tem - 6, 6];
for (int i = 0; i < x.controlData.GetUpperBound(1); i++)
{
for (int j = i + 1; j < x.controlData.GetUpperBound(1); j++)
{
int AABB = 0;
int AABb = 0;
int AaBB = 0;
int AaBb = 0;
int AAbb = 0;
int aaBB = 0;
int aaBb = 0;
int aabb = 0;
int Aabb = 0;
for (int t = 0; t < x.PeoNum; t++)
{
if (x.controlData[t, i] == 0 && x.controlData[t, j] == 0)
{
AABB++;
}
if (x.controlData[t, i] == 0 && x.controlData[t, j] == 1)
{
AABb++;
}
if (x.controlData[t, i] == 1 && x.controlData[t, j] == 0)
{
AaBB++;
}
if (x.controlData[t, i] == 1 && x.controlData[t, j] == 1)
{
AaBb++;
}
if (x.controlData[t, i] == 0 && x.controlData[t, j] == 2)
{
AAbb++;
}
if (x.controlData[t, i] == 2 && x.controlData[t, j] == 0)
{
aaBB++;
}
if (x.controlData[t, i] == 2 && x.controlData[t, j] == 1)
{
aaBb++;
}
if (x.controlData[t, i] == 2 && x.controlData[t, j] == 2)
{
aabb++;
}
if (x.controlData[t, i] == 1 && x.controlData[t, j] == 2)
{
Aabb++;
}
}
double LinkAB = AABB + AABb + AaBB + AaBb;
double PA = (double)(2 * AABB + 2 * AABb + AaBB + 2 * AAbb + Aabb + AaBb) / (2 * x.PeoNum);
double PB = (double)(2 * AABB + AABb + 2 * AaBB + 2 * aaBB + aaBb + AaBb) / (2 * x.PeoNum);
double PAB = 0.25;
double Pab = 0.25;
double PAb = 0.25;
double PaB = 0.25;
double LastPar = 0;
double AB = 0;
double Ab = 0;
par = 0.5;
double DM = 0;
do
{
LastPar = par;
PAB = (2 * AABB + AABb + AaBB + AaBb * par) / (2 * x.PeoNum);
PAb = (2 * AAbb + AABb + Aabb + AaBb * (1 - par)) / (2 * x.PeoNum);
PaB = (2 * aaBB + AaBB + aaBb + AaBb * (1 - par)) / (2 * x.PeoNum);
Pab = (2 * aabb + Aabb + aaBb + AaBb * par) / (2 * x.PeoNum);
par = PAB * Pab / (PAB * Pab + PAb * PaB);
AB = 2 * AABB + AABb + AaBB + AaBb * par;
Ab = 2 * AAbb + AABb + Aabb + AaBb * (1 - par);
} while (Math.Abs(par - LastPar) > 0.000001);
double D = PAB * Pab - PAb * PaB;
if (D > 0)
{
if (PA * (1 - PB) > (1 - PA) * PB)
{
DM = (1 - PA) * PB;
}
else
{
DM = PA * (1 - PB);
}
}
if (D < 0)
{
if (-PA * PB > -(1 - PA) * (1 - PB))
{
DM = -PA * PB;
}
else
{
DM = -(1 - PA) * (1 - PB);
}
}
Dx[i, j] = D / DM;
r2 = D * D / (PAB * PAb * PaB * Pab);
if (r2 < 0.1)
{
continue;
}
else
{
linkageData[i, 0] = i;
linkageData[i, 1] = j;
linkageData[i, 2] = PAB;
linkageData[i, 3] = PAb;
linkageData[i, 4] = PaB;
linkageData[i, 4] = Pab;
}
}
}
}
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);
}
