public void TestExperimentalDesignParserSampleNumbers()
{
RunProteinSignificanceClassifier runProteinSignificanceClassifier = new RunProteinSignificanceClassifier();
int expectedNumberSamples = 8;
int resultNumberSamples = 0;
Dictionary <string, List <string> > resultSamplefileConditionRelation =
runProteinSignificanceClassifier.ExpermientalDesignParser("TestExperimentalDesign.tsv", ref resultNumberSamples);
Assert.AreEqual(expectedNumberSamples, resultNumberSamples);
}
public void TestResizePermutedArray()
{
List <double> expectedResizedArray = new List <double>()
{
0, 1, 2, 3, 5, 6, 7, 9, 10, 12, 13, 14, 16, 17, 18
};
List <double> outputResizedArray = new List <double>();
for (int i = 0; i < 20; i++)
{
outputResizedArray.Add(i);
}
int sizeDifference = 5;
RunProteinSignificanceClassifier runProteinSignificanceClassifier = new RunProteinSignificanceClassifier();
runProteinSignificanceClassifier.ResizePermutedArray(outputResizedArray, sizeDifference);
CollectionAssert.AreEqual(expectedResizedArray, outputResizedArray);
}
public void TestRPCGenerateAllCombinationsOfTwoConditions()
{
RunProteinSignificanceClassifier runProteinSignificanceClassifier = new RunProteinSignificanceClassifier();
List <string> testConditions = new List <string>();
testConditions.Add("condition1");
testConditions.Add("condition2");
testConditions.Add("condition3");
testConditions.Add("condition4");
List <List <string> > expectedConditionPairs = new List <List <string> >();
expectedConditionPairs.Add(new List <string>()
{
"condition1", "condition2"
});
expectedConditionPairs.Add(new List <string>()
{
"condition1", "condition3"
});
expectedConditionPairs.Add(new List <string>()
{
"condition1", "condition4"
});
expectedConditionPairs.Add(new List <string>()
{
"condition2", "condition3"
});
expectedConditionPairs.Add(new List <string>()
{
"condition2", "condition4"
});
expectedConditionPairs.Add(new List <string>()
{
"condition3", "condition4"
});
List <List <string> > resultConditionPairs = runProteinSignificanceClassifier.GenerateAllCombinationsOfTwoConditions(testConditions);
CollectionAssert.AreEqual(expectedConditionPairs, resultConditionPairs);
}
public void TestProteinDataParserSampleFileNames()
{
List <string> expectedSampleFileNames = new List <string>();
expectedSampleFileNames.Add("Intensity_B02_06_161103_A1_HCD_OT_4ul");
expectedSampleFileNames.Add("Intensity_B02_07_161103_A2_HCD_OT_4ul");
expectedSampleFileNames.Add("Intensity_B02_16_161103_A3_HCD_OT_4ul");
expectedSampleFileNames.Add("Intensity_B02_17_161103_A4_HCD_OT_4ul");
expectedSampleFileNames.Add("Intensity_B02_24_161103_C1_HCD_OT_4ul");
expectedSampleFileNames.Add("Intensity_B02_09_161103_C2_HCD_OT_4ul");
expectedSampleFileNames.Add("Intensity_B02_14_161103_C3_HCD_OT_4ul");
expectedSampleFileNames.Add("Intensity_B02_19_161103_C4_HCD_OT_4ul");
int maxAllowedMissingValues = 2;
List <ProteinRowInfo> outputAllProteinInfo = new List <ProteinRowInfo>();
List <string> outputSamplesFileNames = new List <string>();
RunProteinSignificanceClassifier runProteinSignificanceClassifier = new RunProteinSignificanceClassifier();
runProteinSignificanceClassifier.ProteinDataParser(outputAllProteinInfo, maxAllowedMissingValues,
outputSamplesFileNames, "TestQuantifiedProteins.tsv");
CollectionAssert.AreEqual(expectedSampleFileNames, outputSamplesFileNames);
}
public void TestExperimentalDesignParserConditionSampleMapping()
{
RunProteinSignificanceClassifier runProteinSignificanceClassifier = new RunProteinSignificanceClassifier();
Dictionary <string, List <string> > expectedSamplefileConditionRelation = new Dictionary <string, List <string> >();
expectedSamplefileConditionRelation.Add("Ecoli 1x", new List <string>()
{
"Intensity_B02_06_161103_A1_HCD_OT_4ul",
"Intensity_B02_07_161103_A2_HCD_OT_4ul", "Intensity_B02_16_161103_A3_HCD_OT_4ul", "Intensity_B02_17_161103_A4_HCD_OT_4ul"
});
expectedSamplefileConditionRelation.Add("Ecoli 2x", new List <string>()
{
"Intensity_B02_09_161103_C2_HCD_OT_4ul",
"Intensity_B02_14_161103_C3_HCD_OT_4ul", "Intensity_B02_19_161103_C4_HCD_OT_4ul", "Intensity_B02_24_161103_C1_HCD_OT_4ul"
});
int resultNumberSamples = 0;
Dictionary <string, List <string> > resultSamplefileConditionRelation =
runProteinSignificanceClassifier.ExpermientalDesignParser("TestExperimentalDesign.tsv", ref resultNumberSamples);
CollectionAssert.AreEqual(expectedSamplefileConditionRelation, resultSamplefileConditionRelation);
}
public static void Main(string[] args)
{
RunProteinSignificanceClassifier proteinBasedSignificance = new RunProteinSignificanceClassifier();
int numberSamples = 0;
// Parse the ExperimentalDesign File to get info of samples and conditions they belong to
Dictionary <string, List <string> > samplefileConditionRelation = proteinBasedSignificance.ExpermientalDesignParser("C:/Users/Anay/Desktop/UW Madison/Smith Lab/Spectra Data/ExperimentalDesign.tsv"
, ref numberSamples);
// get all conditions and pair them up for Significance classification
List <string> allConditions = new List <string>(samplefileConditionRelation.Keys);
List <List <string> > allTwoConditionCombinations = proteinBasedSignificance.GenerateAllCombinationsOfTwoConditions(allConditions);
foreach (List <string> conditionPair in allTwoConditionCombinations)
{
string firstCondition = conditionPair[0];
string secondCondition = conditionPair[1];
double sOValue = 0.1;
double meanFraction = 0.1;
int maxSignificantCount = 0;
while (meanFraction < 1)
{
while (sOValue < 1)
{
for (int k = 0; k < numberSamples; k++)
{
proteinBasedSignificance = new RunProteinSignificanceClassifier();
//Declaring variables which will be generated after parsing QuantifiedPeptides file
List <ProteinRowInfo> allProteinInfo = new List <ProteinRowInfo>();
List <string> samplesFileNames = new List <string>();
int maxInvalidIntensityValues = k;
proteinBasedSignificance.ProteinDataParser(allProteinInfo, maxInvalidIntensityValues,
samplesFileNames, "C:/Users/Anay/Desktop/UW Madison/Smith Lab/Spectra Data/FlashLFQ_2020-04-26-17-39-35/QuantifiedProteins.tsv");
// imputes missing intensity values for each protein
ImputationProcess imputationProcess = new ImputationProcess();
imputationProcess.RunImputationProcess(allProteinInfo, samplesFileNames, meanFraction);
// Declaring variables which will be generated after T-Tests and Permutation Tests
List <double> observedNValues = new List <double>(); // will store observed N values
List <double> permutedNValues = new List <double>(); // will store permuted N values
StatisticalTests statisticalTests = new StatisticalTests();
// contains proteins and their observed N value, P Value and Log Fold Change
Dictionary <string, List <double> > allProteinObservedStatistics = new Dictionary <string, List <double> >();
// Creating threads for Parallelizing code
ThreadPool.GetMaxThreads(out int workerThreadsCount, out int ioThreadsCount);
int[] threads = Enumerable.Range(0, workerThreadsCount).ToArray();
Parallel.ForEach(threads, (i) =>
{
// Compute observed and permuted N Values for each protein using T Tests and Permutation Testing
for (; i < allProteinInfo.Count; i += workerThreadsCount)
{
ProteinRowInfo proteinRowInfo = allProteinInfo[i];
Dictionary <string, double> samplesintensityData = proteinRowInfo.SamplesIntensityData;
List <string> firstConditionAssociatedSamples = samplefileConditionRelation.GetValueOrDefault(firstCondition);
List <string> secondConditionAssociatedSamples = samplefileConditionRelation.GetValueOrDefault(secondCondition);
List <double> proteinFirstConditionIntensityValues = new List <double>();
List <double> proteinSecondConditionIntensityValues = new List <double>();
// get the protein's intensity values corresponding to the chosen pair of conditions
foreach (string sampleFileName in samplesFileNames)
{
if (firstConditionAssociatedSamples.Contains(sampleFileName))
{
proteinFirstConditionIntensityValues.Add(samplesintensityData[sampleFileName]);
}
if (secondConditionAssociatedSamples.Contains(sampleFileName))
{
proteinSecondConditionIntensityValues.Add(samplesintensityData[sampleFileName]);
}
}
// Compute observed N Values with the chosen pair of conditions using T-Tests and
// store in observedNValues array
List <double> proteinStatistics = statisticalTests.GetNValueUsingTTest(proteinFirstConditionIntensityValues, proteinSecondConditionIntensityValues,
sOValue, false);
// Compute permuted N Values with the chosen pair of conditions using T-Tests and
// store in permutedNValues array
List <double> proteinPermutedNavlues = statisticalTests.GetNValueUsingPermutationtests(proteinFirstConditionIntensityValues,
proteinSecondConditionIntensityValues, sOValue);
// add computed original and permuted statistics for the protein
lock (allProteinObservedStatistics)
{
// add protein and its observed N value, P Value and Log Fold Change in that order
allProteinObservedStatistics.Add(proteinRowInfo.ProteinID, new List <double>()
{
proteinStatistics[0],
proteinStatistics[1], proteinStatistics[2]
});
observedNValues.Add(proteinStatistics[0]);
foreach (double permutedNValue in proteinPermutedNavlues)
{
permutedNValues.Add(permutedNValue);
}
}
}
});
// makes the permuted N values list and the observed N Values list of the same size
proteinBasedSignificance.ResizePermutedArray(permutedNValues, permutedNValues.Count() - observedNValues.Count());
// get the threshold at which we will filter out the significant proteins
double nValueThreshold = statisticalTests.calculateNvaluethreshold(observedNValues, permutedNValues, 0.05);
// determine number of signifcant proteins detected
int newSignificantCount = observedNValues.Count(x => x >= nValueThreshold);
if (newSignificantCount > maxSignificantCount)
{
maxSignificantCount = newSignificantCount;
proteinBasedSignificance.PrintSignificantProtein(allProteinInfo, nValueThreshold, allProteinObservedStatistics,
"C:/Users/Anay/Desktop/UW Madison/Smith Lab/Project 1/ConsoleApp1/ProteinBasedSignificanceModified.csv");
Console.WriteLine("Sig Count - " + maxSignificantCount + "meanFraction - " + meanFraction + "sOValue - "
+ sOValue + "k - " + k);
}
}
sOValue = sOValue + 0.1;
}
sOValue = 0.1;
meanFraction = meanFraction + 0.3;
}
}
}
public void TestProteinDataParserProteinIntensityMapping()
{
List <string> sampleFileNames = new List <string>();
sampleFileNames.Add("Intensity_B02_06_161103_A1_HCD_OT_4ul");
sampleFileNames.Add("Intensity_B02_07_161103_A2_HCD_OT_4ul");
sampleFileNames.Add("Intensity_B02_16_161103_A3_HCD_OT_4ul");
sampleFileNames.Add("Intensity_B02_17_161103_A4_HCD_OT_4ul");
sampleFileNames.Add("Intensity_B02_24_161103_C1_HCD_OT_4ul");
sampleFileNames.Add("Intensity_B02_09_161103_C2_HCD_OT_4ul");
sampleFileNames.Add("Intensity_B02_14_161103_C3_HCD_OT_4ul");
sampleFileNames.Add("Intensity_B02_19_161103_C4_HCD_OT_4ul");
List <ProteinRowInfo> expectedAllProteinInfo = new List <ProteinRowInfo>();
ProteinRowInfo sampleprotein1 = new ProteinRowInfo();
sampleprotein1.ProteinID = "A0A023KES1";
sampleprotein1.SamplesIntensityData["Intensity_B02_06_161103_A1_HCD_OT_4ul"] = 22.192;
sampleprotein1.SamplesIntensityData["Intensity_B02_07_161103_A2_HCD_OT_4ul"] = 22.729;
sampleprotein1.SamplesIntensityData["Intensity_B02_16_161103_A3_HCD_OT_4ul"] = 22.347;
sampleprotein1.SamplesIntensityData["Intensity_B02_17_161103_A4_HCD_OT_4ul"] = 22.397;
sampleprotein1.SamplesIntensityData["Intensity_B02_24_161103_C1_HCD_OT_4ul"] = 23.489;
sampleprotein1.SamplesIntensityData["Intensity_B02_09_161103_C2_HCD_OT_4ul"] = 23.180;
sampleprotein1.SamplesIntensityData["Intensity_B02_14_161103_C3_HCD_OT_4ul"] = 23.293;
sampleprotein1.SamplesIntensityData["Intensity_B02_19_161103_C4_HCD_OT_4ul"] = 23.271;
ProteinRowInfo sampleprotein2 = new ProteinRowInfo();
sampleprotein2.ProteinID = "A0A024R4E5";
sampleprotein2.SamplesIntensityData["Intensity_B02_06_161103_A1_HCD_OT_4ul"] = 25.535;
sampleprotein2.SamplesIntensityData["Intensity_B02_07_161103_A2_HCD_OT_4ul"] = 25.482;
sampleprotein2.SamplesIntensityData["Intensity_B02_16_161103_A3_HCD_OT_4ul"] = 25.308;
sampleprotein2.SamplesIntensityData["Intensity_B02_17_161103_A4_HCD_OT_4ul"] = 25.373;
sampleprotein2.SamplesIntensityData["Intensity_B02_24_161103_C1_HCD_OT_4ul"] = 25.370;
sampleprotein2.SamplesIntensityData["Intensity_B02_09_161103_C2_HCD_OT_4ul"] = 25.368;
sampleprotein2.SamplesIntensityData["Intensity_B02_14_161103_C3_HCD_OT_4ul"] = 25.359;
sampleprotein2.SamplesIntensityData["Intensity_B02_19_161103_C4_HCD_OT_4ul"] = 25.251;
ProteinRowInfo sampleprotein3 = new ProteinRowInfo();
sampleprotein3.ProteinID = "A0A087WTI9";
sampleprotein3.SamplesIntensityData["Intensity_B02_06_161103_A1_HCD_OT_4ul"] = 0;
sampleprotein3.SamplesIntensityData["Intensity_B02_07_161103_A2_HCD_OT_4ul"] = 23.763;
sampleprotein3.SamplesIntensityData["Intensity_B02_16_161103_A3_HCD_OT_4ul"] = 20.783;
sampleprotein3.SamplesIntensityData["Intensity_B02_17_161103_A4_HCD_OT_4ul"] = 20.165;
sampleprotein3.SamplesIntensityData["Intensity_B02_24_161103_C1_HCD_OT_4ul"] = 21.7858;
sampleprotein3.SamplesIntensityData["Intensity_B02_09_161103_C2_HCD_OT_4ul"] = 0;
sampleprotein3.SamplesIntensityData["Intensity_B02_14_161103_C3_HCD_OT_4ul"] = 21.564;
sampleprotein3.SamplesIntensityData["Intensity_B02_19_161103_C4_HCD_OT_4ul"] = 20.469;
expectedAllProteinInfo.Add(sampleprotein1);
expectedAllProteinInfo.Add(sampleprotein2);
expectedAllProteinInfo.Add(sampleprotein3);
int maxAllowedMissingValues = 2;
List <ProteinRowInfo> outputAllProteinInfo = new List <ProteinRowInfo>();
List <string> outputSamplesFileNames = new List <string>();
RunProteinSignificanceClassifier runProteinSignificanceClassifier = new RunProteinSignificanceClassifier();
runProteinSignificanceClassifier.ProteinDataParser(outputAllProteinInfo, maxAllowedMissingValues,
outputSamplesFileNames, "TestQuantifiedProteins.tsv");
foreach (ProteinRowInfo outputProtein in outputAllProteinInfo)
{
if (outputProtein.ProteinID.Equals(sampleprotein1.ProteinID))
{
Assert.That(sampleprotein1.SamplesIntensityData,
Is.EqualTo(outputProtein.SamplesIntensityData).Within(0.001));
}
else if (outputProtein.ProteinID.Equals(sampleprotein2.ProteinID))
{
Assert.That(sampleprotein2.SamplesIntensityData,
Is.EqualTo(outputProtein.SamplesIntensityData).Within(0.001));
}
else if (outputProtein.ProteinID.Equals(sampleprotein3.ProteinID))
{
Assert.That(sampleprotein3.SamplesIntensityData,
Is.EqualTo(outputProtein.SamplesIntensityData).Within(0.001));
}
else
{
Assert.Fail();
}
}
}