private float CalcGoGeneSim(int go, List <int> geneGOSet, GOSimHelper goSimHelper)
{
var maxSim = float.MinValue;
foreach (var geneGO in geneGOSet)
{
var sim = _useGSESAME ? goSimHelper.CalcGOSim_GSESAME(go, geneGO) : goSimHelper.CalcGOSim(go, geneGO); //6355,8150 = Infinity?
if (maxSim < sim)
{
maxSim = (float)sim;
}
}
return(maxSim);
}
private double CalcSimOnDAG_HyperOrCount(string rna1, string rna2, GOSimHelper goSimHelper)
{
double sim = 0;
int count = 0;
var goSet1 = _miRNAs[rna1].GOs;
var goSet2 = _miRNAs[rna2].GOs;
var filteredGOSet1 = goSimHelper.FilterGOs(goSet1);
var filteredGOSet2 = goSimHelper.FilterGOs(goSet2);
if (filteredGOSet1.Count == 0 || filteredGOSet2.Count == 0)
{
return(0.0);
}
Dictionary <int, double> maxSimReverse = new Dictionary <int, double>();
foreach (var go in filteredGOSet2)
{
maxSimReverse[go] = double.MinValue;
}
foreach (var go in filteredGOSet1)
{
double wx = 0;
if (_mode == Mode.Hyper)
{
wx = GetOrSetWeightCache(rna1, go, goSimHelper);
}
else
{
wx = _miRNAs[rna1].kGOAnnotatedCount[go];
count += _miRNAs[rna1].kGOAnnotatedCount[go];
}
var maxSim = float.MinValue;
foreach (var go2 in filteredGOSet2)
{
var sim2 = _useGSESAME ? goSimHelper.CalcGOSim_GSESAME(go, go2) : goSimHelper.CalcGOSim(go, go2);
if (maxSim < sim2)
{
maxSim = (float)sim2;
}
if (maxSimReverse[go2] < sim2)
{
maxSimReverse[go2] = sim2;
}
}
sim += wx * maxSim;
}
foreach (var go in filteredGOSet2)
{
double wx = 0;
if (_mode == Mode.Hyper)
{
wx = GetOrSetWeightCache(rna2, go, goSimHelper);
}
else
{
wx = _miRNAs[rna2].kGOAnnotatedCount[go];
count += _miRNAs[rna2].kGOAnnotatedCount[go];
}
sim += wx * maxSimReverse[go];
}
return(sim / (_mode == Mode.Hyper ? (filteredGOSet1.Count + filteredGOSet2.Count) : count));
}
private double CalcSimOnDAG_Max(string rna1, string rna2, GOSimHelper goSimHelper)
{
double sim = 0;
var goSet1 = _miRNAs[rna1].GOs;
var goSet2 = _miRNAs[rna2].GOs;
var filteredGOSet1 = goSimHelper.FilterGOs(goSet1);
var filteredGOSet2 = goSimHelper.FilterGOs(goSet2);
if (filteredGOSet1.Count == 0 || filteredGOSet2.Count == 0)
{
return(0.0);
}
foreach (var go in filteredGOSet1)
{
foreach (var go2 in filteredGOSet2)
{
var sim2 = _useGSESAME ? goSimHelper.CalcGOSim_GSESAME(go, go2) : goSimHelper.CalcGOSim(go, go2);
if (sim < sim2)
{
sim = (float)sim2;
}
}
}
return(sim);
}