private void GetChromatogramCorrelationData(SipperLcmsTargetedResult result)
{
_chromScanWindowWidth = result.ChromPeakSelected.Width * 2;
var startScan = result.ScanSet.PrimaryScanNumber - (int)Math.Round(_chromScanWindowWidth / 2, 0);
var stopScan = result.ScanSet.PrimaryScanNumber + (int)Math.Round(_chromScanWindowWidth / 2, 0);
result.ChromCorrelationData = _chromatogramCorrelatorTask.CorrelatePeaksWithinIsotopicProfile(result.Run,
NormalizedIso,
startScan,
stopScan);
ChromatogramRSquaredVals.AddRange(
result.ChromCorrelationData.CorrelationDataItems.Select(p => p.CorrelationRSquaredVal.GetValueOrDefault(-1)).
ToList());
//trim off zeros
for (var i = ChromatogramRSquaredVals.Count - 1; i >= 0; i--)
{
if (ChromatogramRSquaredVals[i] <= 0)
{
ChromatogramRSquaredVals.RemoveAt(i);
}
else
{
break;
}
}
result.ChromCorrelationMin = ChromatogramRSquaredVals.Min();
if (ChromatogramRSquaredVals.Count > 1)
{
//get the best rsquared value other than the base peak's rsquared value (which is always 1)
result.ChromCorrelationMax =
(from n in ChromatogramRSquaredVals orderby n descending select n).ToList().ElementAt(1);
result.ChromCorrelationMedian = MathUtils.GetMedian(ChromatogramRSquaredVals);
result.ChromCorrelationAverage = ChromatogramRSquaredVals.Average();
if (ChromatogramRSquaredVals.Count > 2)
{
result.ChromCorrelationStdev = MathUtils.GetStDev(ChromatogramRSquaredVals);
}
else
{
result.ChromCorrelationStdev = -1;
}
}
else
{
result.ChromCorrelationMax = 1;
}
}
private void GetChromatogramCorrelationData(SipperLcmsTargetedResult result)
{
//NOTE: this is a very important step. If too wide, correlation data will be poor
//and may lead to overly strict treatment of the data
_chromScanWindowWidth = result.ChromPeakSelected.Width / 2.35 * 4;
//TODO: change this!
//_chromScanWindowWidth = 19;
var startScan = result.ScanSet.PrimaryScanNumber - (int)Math.Round(_chromScanWindowWidth / 2, 0);
var stopScan = result.ScanSet.PrimaryScanNumber + (int)Math.Round(_chromScanWindowWidth / 2, 0);
result.ChromCorrelationData = _chromatogramCorrelatorTask.CorrelatePeaksWithinIsotopicProfile(result.Run, NormalizedIso, startScan, stopScan);
if (result.ChromCorrelationData.CorrelationDataItems.Count > 0)
{
ChromatogramRSquaredVals.AddRange(result.ChromCorrelationData.CorrelationDataItems.Select(p => p.CorrelationRSquaredVal.GetValueOrDefault(-1)).ToList());
}
//GORD: remove this console code later
//Console.WriteLine();
//Console.WriteLine(result.Target.ID);
//foreach (var item in result.ChromCorrelationData.CorrelationDataItems)
//{
// Console.WriteLine(item.CorrelationRSquaredVal);
//}
//trim off zeros
for (var i = ChromatogramRSquaredVals.Count - 1; i >= 1; i--)
{
if (ChromatogramRSquaredVals[i] <= 0)
{
ChromatogramRSquaredVals.RemoveAt(i);
}
else
{
break;
}
}
if (ChromatogramRSquaredVals.Count > 1)
{
result.ChromCorrelationMin = ChromatogramRSquaredVals.Min();
//get the best rsquared value other than the base peak's rsquared value (which is always 1)
result.ChromCorrelationMax =
(from n in ChromatogramRSquaredVals orderby n descending select n).ToList().ElementAt(1);
result.ChromCorrelationMedian = MathUtils.GetMedian(ChromatogramRSquaredVals);
result.ChromCorrelationAverage = ChromatogramRSquaredVals.Average();
if (ChromatogramRSquaredVals.Count > 2)
{
result.ChromCorrelationStdev = MathUtils.GetStDev(ChromatogramRSquaredVals);
}
else
{
result.ChromCorrelationStdev = -1;
}
}
else
{
result.ChromCorrelationMin = -1;
result.ChromCorrelationMax = -1;
}
}
