private LcmsWarpAlignmentData AlignFeatures(LcmsWarpAlignmentProcessor processor, List <UMCLight> aligneeFeatures, LcmsWarpAlignmentOptions options)
{
var alignmentFunctions = new List <LcmsWarpAlignmentFunction>();
var heatScores = new List <double[, ]>();
var xIntervals = new List <double[]>();
var yIntervals = new List <double[]>();
double minMtdbNet;
double maxMtdbNet;
processor.GetReferenceNetRange(out minMtdbNet, out maxMtdbNet);
var filteredFeatures = FilterFeaturesByAbundance(aligneeFeatures, options).ToList();
// Set features
processor.SetAligneeDatasetFeatures(filteredFeatures);
// Find alignment
processor.PerformAlignmentToMsFeatures();
// Extract alignment function
var alignmentFunction = processor.GetAlignmentFunction();
alignmentFunctions.Add(alignmentFunction);
// Correct the features
processor.ApplyNetMassFunctionToAligneeDatasetFeatures(ref aligneeFeatures);
// Get the heat maps
double[,] heatScore;
double[] xInterval;
double[] yInterval;
processor.GetAlignmentHeatMap(out heatScore, out xInterval, out yInterval);
xIntervals.Add(xInterval);
yIntervals.Add(yInterval);
heatScores.Add(heatScore);
// Get the histograms
double[,] massErrorHistogram;
double[,] netErrorHistogram;
double[,] driftErrorHistogram;
processor.GetErrorHistograms(options.MassBinSize, options.NetBinSize, options.DriftTimeBinSize,
out massErrorHistogram, out netErrorHistogram, out driftErrorHistogram);
// Get the residual data
var residualData = processor.GetResidualData();
var data = new LcmsWarpAlignmentData
{
MassErrorHistogram = massErrorHistogram,
DriftErrorHistogram = driftErrorHistogram,
NetErrorHistogram = netErrorHistogram,
AlignmentFunction = alignmentFunction,
HeatScores = heatScore,
NetIntercept = processor.NetIntercept,
NetRsquared = processor.NetRsquared,
NetSlope = processor.NetSlope,
ResidualData = residualData,
MassMean = processor.MassMu,
MassStandardDeviation = processor.MassStd,
NetMean = processor.NetMu,
NetStandardDeviation = processor.NetStd
};
return(data);
}
