public GroupComparisonResult(GroupComparisonSelector selector, int replicateCount, LinearFitResult linearFitResult, IEnumerable <GroupComparer.RunAbundance> runAbundances)
{
Selector = selector;
LinearFitResult = linearFitResult;
ReplicateCount = replicateCount;
RunAbundances = ImmutableList.ValueOf(runAbundances);
}
public FoldChangeResult(double confidenceLevel, double adjustedPValue, LinearFitResult linearFitResult, double criticalValue) : this()
{
ConfidenceLevel = confidenceLevel;
LinearFit = linearFitResult;
AdjustedPValue = adjustedPValue;
_criticalValue = criticalValue;
}
private void TestGroupComparison(TextReader textReader, bool includeInteraction, IDictionary <string, LinearFitResult> expectedResults)
{
var csvReader = new DsvFileReader(textReader, ',');
var dataRowsByProtein = ToDataRows(ReadCsvFile(csvReader));
Assert.AreNotEqual(0, dataRowsByProtein.Count);
var cache = new QrFactorizationCache();
foreach (var entry in dataRowsByProtein)
{
FoldChangeDataSet dataSet = FoldChangeCalculator.MakeDataSet(entry.Value);
var designMatrix = DesignMatrix.GetDesignMatrix(dataSet, includeInteraction);
var foldChange = designMatrix.PerformLinearFit(cache).First();
LinearFitResult expectedResult = null;
if (null != expectedResults)
{
Assert.IsTrue(expectedResults.TryGetValue(entry.Key, out expectedResult));
}
if (null != expectedResult)
{
Assert.AreEqual(expectedResult.EstimatedValue, foldChange.EstimatedValue, 1E-6);
Assert.AreEqual(expectedResult.DegreesOfFreedom, foldChange.DegreesOfFreedom);
Assert.AreEqual(expectedResult.StandardError, foldChange.StandardError, 1E-6);
Assert.AreEqual(expectedResult.TValue, foldChange.TValue, 1E-6);
Assert.AreEqual(expectedResult.PValue, foldChange.PValue, 1E-6);
}
}
}
private LinearFitResult(LinearFitResult linearFitResult)
{
EstimatedValue = linearFitResult.EstimatedValue;
StandardError = linearFitResult.StandardError;
TValue = linearFitResult.TValue;
DegreesOfFreedom = linearFitResult.DegreesOfFreedom;
PValue = linearFitResult.PValue;
}
private LinearFitResult(LinearFitResult linearFitResult)
{
EstimatedValue = linearFitResult.EstimatedValue;
StandardError = linearFitResult.StandardError;
TValue = linearFitResult.TValue;
DegreesOfFreedom = linearFitResult.DegreesOfFreedom;
PValue = linearFitResult.PValue;
}
public static IDictionary <string, LinearFitResult> ReadExpectedResults(Type type, string resourceName)
{
var result = new Dictionary <string, LinearFitResult>();
using (var reader = GetTextReaderForManifestResource(type, resourceName))
{
var csvReader = new DsvFileReader(reader, ',');
while (null != csvReader.ReadLine())
{
string protein = csvReader.GetFieldByName("Protein");
var linearFitResult = new LinearFitResult(Convert.ToDouble(csvReader.GetFieldByName("log2FC"), CultureInfo.InvariantCulture))
.SetStandardError(Convert.ToDouble(csvReader.GetFieldByName("SE"), CultureInfo.InvariantCulture))
.SetTValue(Convert.ToDouble(csvReader.GetFieldByName("Tvalue"), CultureInfo.InvariantCulture))
.SetDegreesOfFreedom(Convert.ToInt32(csvReader.GetFieldByName("DF"), CultureInfo.InvariantCulture))
.SetPValue(Convert.ToDouble(csvReader.GetFieldByName("pvalue"), CultureInfo.InvariantCulture));
result.Add(protein, linearFitResult);
}
}
return(result);
}
private bool Equals(LinearFitResult other)
{
return(EstimatedValue.Equals(other.EstimatedValue) && StandardError.Equals(other.StandardError) && TValue.Equals(other.TValue) && DegreesOfFreedom == other.DegreesOfFreedom && PValue.Equals(other.PValue));
}
public GroupComparisonResult(GroupComparisonSelector selector, int replicateCount, LinearFitResult linearFitResult)
{
Selector = selector;
LinearFitResult = linearFitResult;
ReplicateCount = replicateCount;
}
private bool Equals(LinearFitResult other)
{
return EstimatedValue.Equals(other.EstimatedValue) && StandardError.Equals(other.StandardError) && TValue.Equals(other.TValue) && DegreesOfFreedom == other.DegreesOfFreedom && PValue.Equals(other.PValue);
}
