public static void GetRatio(SilacEvidence[] silacEvidence, bool[] invertSil, IsotopeMsmsEvidence[] isoEvidence,
bool[] invertIso, RatioType type, out double ratio, out double normalizedRatio,
out int count, out double dev, out int nOutliers, out double pval, int minRatioCount)
{
ratio = 0;
normalizedRatio = 0;
count = 0;
pval = 1;
List <double> lra = new List <double>();
List <double> lnra = new List <double>();
for (int i = 0; i < silacEvidence.Length; i++)
{
SilacEvidence se = silacEvidence[i];
double r = se.GetRatio(type);
if (r > 0 && !double.IsInfinity(r) && !double.IsNaN(r))
{
lra.Add(invertSil[i] ? -Math.Log(r) : Math.Log(r));
lnra.Add(invertSil[i] ? -Math.Log(se.GetNormalizedRatio(type)) : Math.Log(se.GetNormalizedRatio(type)));
count++;
}
}
for (int i = 0; i < isoEvidence.Length; i++)
{
IsotopeMsmsEvidence se = isoEvidence[i];
double r = se.GetRatio(type);
if (r > 0 && !double.IsInfinity(r) && !double.IsNaN(r))
{
lra.Add(invertIso[i] ? -Math.Log(r) : Math.Log(r));
lnra.Add(invertIso[i] ? -Math.Log(se.GetNormalizedRatio(type)) : Math.Log(se.GetNormalizedRatio(type)));
count++;
}
}
if (lra.Count >= minRatioCount)
{
ratio = ArrayUtil.Median(lra.ToArray());
}
if (lra.Count > 1 && lra.Count >= minRatioCount)
{
double dummy;
new OneSampleTTest().Test(lnra.ToArray(), 0, out dummy, out pval, out dummy, out dummy);
}
if (lnra.Count > 0 && lnra.Count >= minRatioCount)
{
normalizedRatio = ArrayUtil.Median((lnra.ToArray()));
}
if (count < minRatioCount)
{
ratio = double.NaN;
normalizedRatio = double.NaN;
dev = double.NaN;
nOutliers = 0;
pval = double.NaN;
return;
}
if (count > 1 && count >= minRatioCount)
{
List <double> lnvals = new List <double>();
for (int i = 0; i < silacEvidence.Length; i++)
{
SilacEvidence se = silacEvidence[i];
double nr = se.GetNormalizedRatio(type);
if (nr > 0 && !double.IsInfinity(nr) && !double.IsNaN(nr))
{
double lnr = Math.Log(nr);
lnvals.Add(invertSil[i] ? -lnr : lnr);
}
}
for (int i = 0; i < isoEvidence.Length; i++)
{
IsotopeMsmsEvidence se = isoEvidence[i];
double nr = se.GetNormalizedRatio(type);
if (nr > 0 && !double.IsInfinity(nr) && !double.IsNaN(nr))
{
double lnr = Math.Log(nr);
lnvals.Add(invertIso[i] ? -lnr : lnr);
}
}
NumUtil.CountOutliers(lnvals.ToArray(), out nOutliers);
dev = 100 * Math.Sqrt(ArrayUtil.Variance(lnvals.ToArray()));
}
else
{
dev = double.NaN;
nOutliers = 0;
}
ratio = Math.Exp(ratio);
normalizedRatio = Math.Exp(normalizedRatio);
}
