public Tuple <double, int, int[]> Compute_mHG(mHGCorrectionType correctionType, ConfigParams Conf)
{
lock (locker)
{
_mHG = mHGJumper.minimumHypergeometric(InducedLabledVector, -1, -1, correctionType);
Conf.mHGlist.Add(new Tuple <double, int>(mHG.Item1, Interlocked.Increment(ref Conf.computedMHGs)));
}
return(_mHG);
}
public static Tuple <double, int, int[]> minimumHypergeometric(bool[] binVec, int tN = -1, int tB = -1, mHGCorrectionType correctMultiHypothesis = mHGCorrectionType.Exact)
{
var N = tN > 0 ? tN : binVec.Length;
var K = tB > 0 ? tB : binVec.Sum(val => val ? 1 : 0);
var B = tB > 0 ? tB : binVec.Sum(val => !val ? 1 : 0);
var currHGT = 1.0;
var mHGT = 1.1;
var currIndex = 0;
var k = 0;
//OptDistVec is a vector that counts for each '1' in the binary vector the minimum number of 1's needed directly after it for a significant p-value
var OptDistVec = new int[Ones + 1];
for (var i = 0; i < Ones + 1; i++)
{
OptDistVec[i] = Ones; // default max step size (int.maxvalue)
}
for (var i = 0; i < Ones + 1; i++)
{
if (HGTmat[1, i] <= optHGT.Value)
{
OptDistVec[0] = Math.Min(OptDistVec[0], i);
}
}
for (var n = 0; n < binVec.Length; n++)
{
if (binVec[n])
{
k++;
currHGT = HGTmat[n - k + 1, k];
//currHGT = ScoreMap[currHG];
if (currHGT < mHGT)
{
currIndex = n;
mHGT = currHGT;
}
//check distance to optimum
if (optHGT.HasValue && optHGT <= currHGT)
{
for (var i = k; i < Ones + 1; i++)
{
if (HGTmat[n - k + 1, i] <= optHGT.Value)
{
OptDistVec[k] = Math.Min(OptDistVec[k], i - k);
}
}
}
else
{
optHGT = currHGT;
Console.WriteLine("new mHG OPT={0}", optHGT);
}
}
}
//for (var i = 0; i < Ones; i++) if(OptDistVec[i] > Ones) OptDistVec[i] = 1; //this happens when we cannot fulfil the required number of ones at this threshold.
double pval = -1;
switch (correctMultiHypothesis)
{
case mHGCorrectionType.Exact:
pval = ScoreMap[mHGT];
break;
case mHGCorrectionType.None:
pval = mHGT;
break;
case mHGCorrectionType.Bonferroni:
pval = mHGT * N;
break;
case mHGCorrectionType.Lipson:
pval = mHGT * B;
break;
}
return(new Tuple <double, int, int[]>(pval, currIndex + 1, OptDistVec));
}
