public static IHypothesisTestingTwoSample CreateTests(HypothesisTests test)
{
IHypothesisTestingTwoSample newTest = null;
switch (test)
{
case HypothesisTests.TTest:
newTest = new StudentTTest();
break;
case HypothesisTests.MannWhitneyU:
newTest = new MannWhitneyTest();
break;
case HypothesisTests.KolmogorovSmirnov:
newTest = new KolmogorovSmirnovTest();
break;
}
return(newTest);
}
public void TestSpectralAlignment(string basePath, string baselineName, string aligneeName,
double comparisonCutoff)
{
RootDataPath = basePath;
var featureFileX = GetTestPath(baselineName + "_isos.csv");
var rawFileX = GetTestPath(baselineName + ".raw");
var featureFileY = GetTestPath(aligneeName + "_isos.csv");
var rawFileY = GetTestPath(aligneeName + ".raw");
Print("Detecting Features");
var baselineFeatures = FindFeatures(rawFileX, featureFileX);
var aligneeFeatures = FindFeatures(rawFileY, featureFileY);
Print("Aligning Features");
// Align the features
var aligner = new LcmsWarpFeatureAligner();
var alignmentOptions = new AlignmentOptions();
aligner.Options = alignmentOptions.LCMSWarpOptions;
aligner.Align(baselineFeatures, aligneeFeatures);
PrintFeatureMsMsData(baselineFeatures);
PrintFeatureMsMsData(aligneeFeatures);
var matches = GetSpectralMatches(
baselineFeatures, aligneeFeatures, comparisonCutoff);
Print(string.Format("Found {0} spectral matches", matches.Count));
Print("Similarity, Pre-Alignment, Post-Alignment");
var counts = new Dictionary<double, int>();
counts.Add(.9, 0);
counts.Add(.8, 0);
counts.Add(.7, 0);
counts.Add(.6, 0);
counts.Add(.5, 0);
var preDist = new List<double>();
var postDist = new List<double>();
foreach (var match in matches)
{
var baselineFeature = match.Baseline.ParentFeature.ParentFeature;
var aligneeFeature = match.Alignee.ParentFeature.ParentFeature;
var preAlignment = baselineFeature.Net - aligneeFeature.Net;
var postAlignment = baselineFeature.Net - aligneeFeature.NetAligned;
postDist.Add(postAlignment);
preDist.Add(preAlignment);
Print(string.Format("{0},{1},{2}", match.Similarity, preAlignment, postAlignment));
if (match.Similarity > .9)
{
counts[.9]++;
}
else if (match.Similarity > .8)
{
counts[.8]++;
}
else if (match.Similarity > .7)
{
counts[.7]++;
}
else if (match.Similarity > .6)
{
counts[.6]++;
}
}
Print("");
Print("Counts");
Print("");
foreach (var key in counts.Keys)
{
Print(string.Format("{0},{1}", key, counts[key]));
}
var test = new MannWhitneyTest();
var data = test.Test(preDist, postDist);
Print(string.Format("Two Tail - {0} ", data.TwoTail));
Print(string.Format("Left Tail - {0} ", data.LeftTail));
Print(string.Format("Right Tail - {0} ", data.RightTail));
}
public void TestSpectralAlignment(string basePath, string baselineName, string aligneeName,
double comparisonCutoff)
{
RootDataPath = basePath;
var featureFileX = GetTestPath(baselineName + "_isos.csv");
var rawFileX = GetTestPath(baselineName + ".raw");
var featureFileY = GetTestPath(aligneeName + "_isos.csv");
var rawFileY = GetTestPath(aligneeName + ".raw");
Print("Detecting Features");
var baselineFeatures = FindFeatures(rawFileX, featureFileX);
var aligneeFeatures = FindFeatures(rawFileY, featureFileY);
Print("Aligning Features");
// Align the features
var alignmentOptions = new AlignmentOptions();
var aligner = new LcmsWarpFeatureAligner(alignmentOptions.LCMSWarpOptions);
aligner.Align(baselineFeatures, aligneeFeatures);
PrintFeatureMsMsData(baselineFeatures);
PrintFeatureMsMsData(aligneeFeatures);
var matches = GetSpectralMatches(
baselineFeatures, aligneeFeatures, comparisonCutoff);
Print(string.Format("Found {0} spectral matches", matches.Count));
Print("Similarity, Pre-Alignment, Post-Alignment");
var counts = new Dictionary <double, int>();
counts.Add(.9, 0);
counts.Add(.8, 0);
counts.Add(.7, 0);
counts.Add(.6, 0);
counts.Add(.5, 0);
var preDist = new List <double>();
var postDist = new List <double>();
foreach (var match in matches)
{
var baselineFeature = match.Baseline.ParentFeature.GetParentFeature();
var aligneeFeature = match.Alignee.ParentFeature.GetParentFeature();
var preAlignment = baselineFeature.Net - aligneeFeature.Net;
var postAlignment = baselineFeature.Net - aligneeFeature.NetAligned;
postDist.Add(postAlignment);
preDist.Add(preAlignment);
Print(string.Format("{0},{1},{2}", match.Similarity, preAlignment, postAlignment));
if (match.Similarity > .9)
{
counts[.9]++;
}
else if (match.Similarity > .8)
{
counts[.8]++;
}
else if (match.Similarity > .7)
{
counts[.7]++;
}
else if (match.Similarity > .6)
{
counts[.6]++;
}
}
Print("");
Print("Counts");
Print("");
foreach (var key in counts.Keys)
{
Print(string.Format("{0},{1}", key, counts[key]));
}
var test = new MannWhitneyTest();
var data = test.Test(preDist, postDist);
Print(string.Format("Two Tail - {0} ", data.TwoTail));
Print(string.Format("Left Tail - {0} ", data.LeftTail));
Print(string.Format("Right Tail - {0} ", data.RightTail));
}
