/// <summary>
/// Uses a list of MassTagLights as a baseline for aligning a list of UMCLights to it, using
/// the passed in options for processor options as well as a boolean for whether to align based on
/// Drift Times as well.
/// Creates an LCMS Alignment processor to do the alignment, does the alignment, and then passes
/// back the alignment data to the caller.
/// </summary>
/// <param name="massTags"></param>
/// <param name="aligneeFeatures"></param>
/// <param name="options"></param>
/// <returns></returns>
private LcmsWarpAlignmentData AlignFeatures(List <MassTagLight> massTags, List <UMCLight> aligneeFeatures,
LcmsWarpAlignmentOptions options)
{
var alignmentProcessor = new LcmsWarpAlignmentProcessor
{
Options = options
};
alignmentProcessor.ApplyAlignmentOptions();
alignmentProcessor.Progress += alignmentProcessor_Progress;
var featureTest = aligneeFeatures.Find(x => x.DriftTime > 0);
var massTagTest = massTags.Find(x => x.DriftTime > 0);
if (featureTest != null && massTagTest == null)
{
Console.WriteLine("Warning! Data has drift time info, but the mass tags do not.");
}
alignmentProcessor.SetReferenceDatasetFeatures(massTags);
var data = AlignFeatures(alignmentProcessor, aligneeFeatures, options);
return(data);
}
/// <summary>
/// Public constructor for the LCMS Alignment Processor
/// Initializes a new LCMSWarp object using the LCMS Alignment options
/// which were passed into the Processor
/// </summary>
public LcmsWarpAlignmentProcessor()
{
m_lcmsWarp = new LcmsWarp();
Options = new LcmsWarpAlignmentOptions();
ApplyAlignmentOptions();
AligningToMassTagDb = false;
}
public LcmsWarpAdapter(LcmsWarpAlignmentOptions options)
{
m_options = options;
}
private static IEnumerable <UMCLight> FilterFeaturesByAbundance(List <UMCLight> features, LcmsWarpAlignmentOptions options)
{
// Sort by abundance to ease filtering process. Options look at the percentage of abundance
// so threshhold needs to be converted to what the abundance sum would be.
features.Sort((x, y) => x.AbundanceSum.CompareTo(y.AbundanceSum));
var percent = 1 - (options.TopFeatureAbundancePercent / 100);
var total = features.Count - Convert.ToInt32(features.Count * percent);
var threshhold = features[Math.Min(features.Count - 1, Math.Max(0, total))].AbundanceSum;
// Re-sort with regards to monoisotopic mass for accurate application of NET-Mass function
// to the dataset we need to align.
features.Sort((x, y) => x.MassMonoisotopic.CompareTo(y.MassMonoisotopic));
if (threshhold <= 0)
{
return(features);
}
//Filters features below the threshold
var filteredFeatures = features.Where(feature => feature.AbundanceSum >= threshhold);
return(filteredFeatures);
}
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);
}
/// <summary>
/// Uses a list of UMCLights as a baseline for aligning a second list of UMCLights to it, using
/// the passed in options for processor options
/// Creates an LCMS Alignment processor to do the alignment, does the alignment, and then passes
/// back the alignment data to the caller.
/// </summary>
/// <param name="baseline"></param>
/// <param name="aligneeFeatures"></param>
/// <param name="options"></param>
/// <returns></returns>
private LcmsWarpAlignmentData AlignFeatures(List <UMCLight> baseline, List <UMCLight> aligneeFeatures, LcmsWarpAlignmentOptions options)
{
var alignmentProcessor = new LcmsWarpAlignmentProcessor
{
Options = options
};
alignmentProcessor.ApplyAlignmentOptions();
alignmentProcessor.Progress += alignmentProcessor_Progress;
var filteredBaselineFeatures = FilterFeaturesByAbundance(baseline, options) as List <UMCLight>;
alignmentProcessor.SetReferenceDatasetFeatures(filteredBaselineFeatures);
return(AlignFeatures(alignmentProcessor, aligneeFeatures, options));
}
