[InlineData(1e-6)] // Background should not be counted
public void StepNotMoreThanStepCount(double tauW)
{
// Arrange
var s1 = new Bed <Peak>();
s1.Add(new Peak(10, 20, 1E-4), _chr, _strand);
s1.Add(new Peak(30, 40, 1E-5), _chr, _strand);
s1.Add(new Peak(50, 60, 1E-6), _chr, _strand);
s1.Add(new Peak(70, 80, 1E-7), _chr, _strand);
s1.Add(new Peak(90, 99, 1E-8), _chr, _strand);
var s2 = new Bed <Peak>();
s2.Add(new Peak(11, 18, 1E-4), _chr, _strand);
s2.Add(new Peak(33, 38, 1E-5), _chr, _strand);
s2.Add(new Peak(55, 58, 1E-6), _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, s1);
mspc.AddSample(1, s2);
var messages = new List <ProgressReport>();
mspc.StatusChanged += (object sender, ValueEventArgs e) => messages.Add(e.Value);
// Act
mspc.RunAsync(new Config(ReplicateType.Biological, tauW, tauW, tauW, 2, 0.05F, MultipleIntersections.UseLowestPValue));
mspc.Done.WaitOne();
// Assert
Assert.DoesNotContain(messages, x => x.Step > x.StepCount);
}
public void T1()
{
// Arrange
var sA = new Bed <Peak>();
var r11 = new Peak(left: 10, right: 20, value: 1e-4, name: "r11");
sA.Add(r11, _chr, _strand);
var sB = new Bed <Peak>();
sB.Add(new Peak(left: 5, right: 12, value: 1e-4, name: "r21"), _chr, _strand);
sB.Add(new Peak(left: 18, right: 25, value: 1e-4, name: "r22"), _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-3, 1e-8, 1e-8, 2, 1F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
Assert.True(res[0].Chromosomes[_chr].Get(Attributes.Discarded).Count() == 1);
Assert.False(res[0].Chromosomes[_chr].Get(Attributes.Confirmed).Any());
Assert.True(res[0].Chromosomes[_chr].Get(Attributes.Discarded).ToList()[0].Source.CompareTo(r11) == 0);
}
public void ComputeAdjustedPValue()
{
var sA = new Bed <Peak>();
sA.Add(new Peak(left: 10, right: 20, value: 0.01), _chr, _strand);
sA.Add(new Peak(left: 100, right: 200, value: 0.001), _chr, _strand);
var sB = new Bed <Peak>();
sB.Add(new Peak(left: 5, right: 12, value: 0.01), _chr, _strand);
sB.Add(new Peak(left: 50, right: 120, value: 0.001), _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-1, 1e-2, 1e-2, 2, 0.05F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
Assert.True(res[0].Chromosomes[_chr].Get(Attributes.TruePositive).First().AdjPValue == 0.01);
Assert.True(res[0].Chromosomes[_chr].Get(Attributes.TruePositive).Last().AdjPValue == 0.002);
}
private Mspc <Peak> InitializeMSPC()
{
var sA = new Bed <Peak>();
sA.Add(r11, "chr1", '*');
sA.Add(r12, "chr1", '*');
var sB = new Bed <Peak>();
sB.Add(r21, "chr1", '*');
sB.Add(r22, "chr1", '*');
sB.Add(r23, "chr1", '*');
var sC = new Bed <Peak>();
sC.Add(r31, "chr1", '*');
sC.Add(r32, "chr1", '*');
sC.Add(r33, "chr1", '*');
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
mspc.AddSample(2, sC);
return(mspc);
}
public void AssignFalsePositive()
{
var sA = new Bed <Peak>();
sA.Add(new Peak(left: 10, right: 20, value: 1e-6), _chr, _strand);
sA.Add(new Peak(left: 100, right: 200, value: 1e-8), _chr, _strand);
sA.Add(new Peak(left: 1000, right: 2000, value: 1e-10), _chr, _strand);
sA.Add(new Peak(left: 10000, right: 20000, value: 1e-12), _chr, _strand);
var sB = new Bed <Peak>();
sB.Add(new Peak(left: 5, right: 12, value: 1e-7), _chr, _strand);
sB.Add(new Peak(left: 50, right: 120, value: 1e-9), _chr, _strand);
sB.Add(new Peak(left: 500, right: 1200, value: 1e-11), _chr, _strand);
sB.Add(new Peak(left: 5000, right: 12000, value: 1e-13), _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-4, 1e-6, 1e-6, 2, 5e-10F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
foreach (var sample in res)
{
Assert.True(sample.Value.Chromosomes[_chr].Count(Attributes.FalsePositive) == 2);
}
}
private Mspc SetupMSPC(int peakCount = 4, float alpha = 5e-10F)
{
var sA = new Bed <Peak>();
for (int i = 0; i < peakCount; i++)
{
sA.Add(_setA[i], _chrs[i], _strand);
}
var sB = new Bed <Peak>();
for (int i = 0; i < peakCount; i++)
{
sB.Add(_setB[i], _chrs[i], _strand);
}
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-4, 1e-8, 1e-8, 2, alpha, MultipleIntersections.UseLowestPValue);
mspc.Run(config);
return(mspc);
}
public void DoNotCountOverlapsFromSameSample()
{
// Arrange
var sA = new Bed <Peak>();
sA.Add(new Peak(left: 10, right: 20, value: 0.01, hashSeed: "0"), "chr1", '*');
sA.Add(new Peak(left: 10, right: 20, value: 0.01, hashSeed: "1"), "chr1", '*');
sA.Add(new Peak(left: 10, right: 20, value: 0.01, hashSeed: "2"), "chr1", '*');
sA.Add(new Peak(left: 10, right: 20, value: 0.01, hashSeed: "3"), "chr1", '*');
var sB = new Bed <Peak>();
sB.Add(new Peak(left: 5, right: 12, value: 0.01), "chr1", '*');
var sC = new Bed <Peak>();
sC.Add(new Peak(left: 18, right: 25, value: 0.01), "chr1", '*');
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
mspc.AddSample(2, sC);
var config = new Config(ReplicateType.Biological, 1, 1, 1, 5, 1F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
Assert.True(res[0].Chromosomes["chr1"].Count(Attributes.Confirmed) == 0);
}
public void AssertCorrectPeakIsTaggedAsFalsePositive()
{
var sA = new Bed <Peak>();
var r11 = new Peak(left: 10, right: 20, value: 1e-6);
sA.Add(r11, _chr, _strand);
sA.Add(new Peak(left: 100, right: 200, value: 1e-8), _chr, _strand);
sA.Add(new Peak(left: 1000, right: 2000, value: 1e-10), _chr, _strand);
sA.Add(new Peak(left: 10000, right: 20000, value: 1e-12), _chr, _strand);
var sB = new Bed <Peak>();
sB.Add(new Peak(left: 5, right: 12, value: 1e-7), _chr, _strand);
sB.Add(new Peak(left: 50, right: 120, value: 1e-9), _chr, _strand);
sB.Add(new Peak(left: 500, right: 1200, value: 1e-11), _chr, _strand);
sB.Add(new Peak(left: 5000, right: 12000, value: 1e-13), _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-4, 1e-6, 1e-6, 2, 5e-10F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
Assert.True(res[0].Chromosomes[_chr].Get(Attributes.FalsePositive).First().Source.Equals(r11));
}
public void StringentNonOverlappingPeaks()
{
// Arrange
var sA = new Bed <Peak>();
sA.Add(new Peak(left: 10, right: 20, value: 1e-9), _chr, _strand);
var sB = new Bed <Peak>();
sB.Add(new Peak(left: 50, right: 60, value: 1e-12), _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-4, 1e-8, 1e-4, 2, 1F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
foreach (var s in res)
{
Assert.True(s.Value.Chromosomes[_chr].Count(Attributes.Stringent) == 1);
}
}
public void ThreePeaksTwoOverlapping(int c, int expected)
{
// Arrange
var sA = new Bed <Peak>();
sA.Add(new Peak(left: 10, right: 20, value: 0.01), "chr1", '*');
var sB = new Bed <Peak>();
sB.Add(new Peak(left: 5, right: 12, value: 0.01), "chr1", '*');
var sC = new Bed <Peak>();
sC.Add(new Peak(left: 18, right: 25, value: 0.01), "chr1", '*');
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
mspc.AddSample(2, sC);
var config = new Config(ReplicateType.Biological, 1, 1, 1, c, 1F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
Assert.True(new[]
{
res[0].Chromosomes["chr1"].Get(Attributes.Confirmed).Count(),
res[1].Chromosomes["chr1"].Get(Attributes.Confirmed).Count(),
res[2].Chromosomes["chr1"].Get(Attributes.Confirmed).Count()
}.All(x => x == expected));
}
public void OnlyOnePeakPerSampleIsConsideredForC()
{
// Arrange
var sA = new Bed <Peak>();
sA.Add(new Peak(left: 10, right: 20, value: 0.01), "chr1", '*');
var sB = new Bed <Peak>();
sB.Add(new Peak(left: 5, right: 12, value: 0.01), "chr1", '*');
sB.Add(new Peak(left: 14, right: 22, value: 0.01), "chr1", '*');
var sC = new Bed <Peak>();
sC.Add(new Peak(left: 24, right: 25, value: 0.01), "chr1", '*');
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
mspc.AddSample(2, sC);
var config = new Config(ReplicateType.Biological, 1, 1, 1, 3, 1F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
Assert.False(res[0].Chromosomes["chr1"].Get(Attributes.Confirmed).Any());
}
public void BackgroundOverlappingNonBackground()
{
// Arrange
var sA = new Bed <Peak>();
sA.Add(new Peak(left: 10, right: 20, value: 1e-2), _chr, _strand);
var sB = new Bed <Peak>();
sB.Add(new Peak(left: 50, right: 60, value: 1e-8), _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-4, 1e-8, 1e-4, 2, 1F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
Assert.True(
res[0].Chromosomes[_chr].Count(Attributes.Background) == 1 &&
res[1].Chromosomes[_chr].Count(Attributes.Background) == 0);
}
public void ConfirmTwoPeaksWithVeryLowPValue()
{
// Arrange
var sA = new Bed <Peak>();
var sAP = new Peak(left: 10, right: 20, value: 5e-321);
sA.Add(sAP, _chr, _strand);
var sB = new Bed <Peak>();
var sBP = new Peak(left: 5, right: 15, value: 5e-323);
sB.Add(sBP, _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-4, 1e-8, 1e-8, 2, 1F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
Assert.True(
res[0].Chromosomes[_chr].Get(Attributes.Confirmed).Any() &&
res[1].Chromosomes[_chr].Get(Attributes.Confirmed).Any());
}
public void IntervalsWithExactSameCoordinates()
{
// Arrange
int sampleCount = 22;
var mspc = new Mspc();
for (uint i = 0; i < sampleCount - 2; i++)
{
var bed = new Bed <Peak>();
bed.Add(new Peak(10, 20, 0.01), "chr1", '*');
mspc.AddSample(i, bed);
}
var bedB = new Bed <Peak>();
bedB.Add(new Peak(8, 12, 0.01), "chr1", '*');
mspc.AddSample((uint)sampleCount - 2, bedB);
var bedC = new Bed <Peak>();
bedC.Add(new Peak(18, 25, 0.01), "chr1", '*');
mspc.AddSample((uint)sampleCount - 1, bedC);
var config = new Config(ReplicateType.Biological, 1, 1, 1, sampleCount, 1F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
for (uint i = 0; i < sampleCount; i++)
{
Assert.True(res[i].Chromosomes["chr1"].Count(Attributes.Confirmed) == 1);
}
}
public void ProcessedStringentPeakEqualsInput()
{
// Arrange
var sA = new Bed <Peak>();
var sAP = new Peak(left: 10, right: 20, value: 1e-9);
sA.Add(sAP, _chr, _strand);
var sB = new Bed <Peak>();
var sBP = new Peak(left: 50, right: 60, value: 1e-12);
sB.Add(sBP, _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-4, 1e-8, 1e-4, 2, 1F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
Assert.True(
res[0].Chromosomes[_chr].Get(Attributes.Stringent).ToList()[0].Source.Equals(sAP) &&
res[1].Chromosomes[_chr].Get(Attributes.Stringent).ToList()[0].Source.Equals(sBP));
}
private bool Run(List <Bed <Peak> > samples, Config config, out Mspc mspc)
{
try
{
_logger.LogStartOfASection("Analyzing Samples");
mspc = new Mspc()
{
DegreeOfParallelism = _degreeOfParallelism
};
mspc.StatusChanged += _logger.LogMSPCStatus;
foreach (var sample in samples)
{
mspc.AddSample(sample.FileHashKey, sample);
}
mspc.RunAsync(config);
mspc.Done.WaitOne();
return(true);
}
catch (Exception e)
{
mspc = null;
_logger.LogException(e);
Environment.ExitCode = 1;
return(false);
}
}
private ReadOnlyDictionary <uint, Result <Peak> > RunMSPCAndReturnResult(Config config)
{
var sA = new Bed <Peak>();
sA.Add(new Peak(left: 10, right: 20, value: 1E-5), _chr, _strand);
var sB = new Bed <Peak>();
sB.Add(new Peak(left: 12, right: 18, value: 1E-5), _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
return(mspc.Run(config));
}
public void FivePeaksThreeOverlapping()
{
// Arrange
var sA = new Bed <Peak>();
sA.Add(new Peak(left: 10, right: 20, value: 0.01), "chr1", '*');
var sB = new Bed <Peak>();
sB.Add(new Peak(left: 5, right: 18, value: 0.01), "chr1", '*');
var sC = new Bed <Peak>();
sC.Add(new Peak(left: 14, right: 25, value: 0.01), "chr1", '*');
var sD = new Bed <Peak>();
sD.Add(new Peak(left: 35, right: 40, value: 0.01), "chr1", '*');
var sE = new Bed <Peak>();
sE.Add(new Peak(left: 43, right: 50, value: 0.01), "chr1", '*');
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
mspc.AddSample(2, sC);
mspc.AddSample(3, sD);
mspc.AddSample(4, sE);
var config = new Config(ReplicateType.Biological, 1, 1, 1, 1, 1F, MultipleIntersections.UseLowestPValue);
// Act
var res = mspc.Run(config);
// Assert
Assert.True(new[]
{
res[0].Chromosomes["chr1"].Get(Attributes.Confirmed).Count(),
res[1].Chromosomes["chr1"].Get(Attributes.Confirmed).Count(),
res[2].Chromosomes["chr1"].Get(Attributes.Confirmed).Count(),
res[3].Chromosomes["chr1"].Get(Attributes.Confirmed).Count(),
res[4].Chromosomes["chr1"].Get(Attributes.Confirmed).Count()
}.All(x => x == 1));
}
private Mspc InitializeMSPC()
{
/// r11 r12
/// Sample 0: --░░░░░░░░░░░-------████████████----------------------------
/// r21 r22 r23
/// Sample 1: ---------████████████████----▒▒▒▒▒▒▒▒---▒▒▒▒▒▒▒▒------------
/// r31 r32 r33
/// Sample 2: ▒▒▒▒---██████████---------------------------------████████--
///
/// Legend: [░░ Background peak], [▒▒ Weak peak], [██ Stringent peak]
var r11 = new Peak(left: 3, right: 13, value: 1e-2, summit: 10, name: "r11");
var r12 = new Peak(left: 21, right: 32, value: 1e-12, summit: 25, name: "r12");
var r21 = new Peak(left: 10, right: 25, value: 1e-8, summit: 20, name: "r21");
var r22 = new Peak(left: 30, right: 37, value: 1e-5, summit: 35, name: "r22");
var r23 = new Peak(left: 41, right: 48, value: 1e-6, summit: 45, name: "r23");
var r31 = new Peak(left: 0, right: 4, value: 1e-6, summit: 2, name: "r31");
var r32 = new Peak(left: 8, right: 17, value: 1e-12, summit: 12, name: "r32");
var r33 = new Peak(left: 51, right: 58, value: 1e-18, summit: 55, name: "r33");
var sA = new Bed <Peak>();
sA.Add(r11, _chr, _strand);
sA.Add(r12, _chr, _strand);
var sB = new Bed <Peak>();
sB.Add(r21, _chr, _strand);
sB.Add(r22, _chr, _strand);
sB.Add(r23, _chr, _strand);
var sC = new Bed <Peak>();
sC.Add(r31, _chr, _strand);
sC.Add(r32, _chr, _strand);
sC.Add(r33, _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
mspc.AddSample(2, sC);
return(mspc);
}
internal void Run()
{
foreach (var sample in _samples)
{
_mspc.AddSample(sample.FileHashKey, sample);
}
_mspc.RunAsync(_options);
_mspc.Done.WaitOne();
}
public void NumberOfPeaks()
{
// Arrange
var mspc = new Mspc();
mspc.AddSample(0, CreateSample(0, 20, 1000));
mspc.AddSample(1, CreateSample(2, 20, 2000));
// Act
var res = mspc.Run(new Config(
ReplicateType.Biological, 1e-4, 1e-5, 1e-5, 1, 0.05F, MultipleIntersections.UseLowestPValue));
// Assert
for (int c = 0; c < 20; c++)
{
Assert.True(res[0].Chromosomes["chr" + c].Get(Attributes.Confirmed).Count() == 1000);
Assert.True(res[1].Chromosomes["chr" + c].Get(Attributes.Confirmed).Count() == 2000);
}
}
private ReadOnlyDictionary <uint, Result <Peak> > GenerateAndProcessStringentPeaks()
{
var sA = new Bed <Peak>();
sA.Add(new Peak(left: 10, right: 20, value: 1e-9), _chr, _strand);
var sB = new Bed <Peak>();
sB.Add(new Peak(left: 5, right: 12, value: 1e-12), _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-4, 1e-8, 1e-4, 2, 1F, MultipleIntersections.UseLowestPValue);
// Act
return(mspc.Run(config));
}
private ReadOnlyDictionary <uint, Result <Peak> > InitializeAndRun(MultipleIntersections miChoice)
{
// Arrange
var sA = new Bed <Peak>();
sA.Add(r11, _chr, _strand);
var sB = new Bed <Peak>();
sB.Add(r21, _chr, _strand);
sB.Add(r22, _chr, _strand);
sB.Add(r23, _chr, _strand);
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
// Act
return(mspc.Run(new Config(ReplicateType.Biological, 1e-4, 1e-8, 1e-8, 2, 1F, miChoice)));
}
public void MergeTwoConsensusPeaks(int xLeft, int xRight, int yLeft, int yRight, int cLeft, int cRight)
{
// Arrange
var mspc = new Mspc();
var sA = new Bed <Peak>();
sA.Add(new Peak(left: xLeft, right: xRight, value: 0.01), _chr, _strand);
mspc.AddSample(0, sA);
var sB = new Bed <Peak>();
sB.Add(new Peak(left: yLeft, right: yRight, value: 0.01), _chr, _strand);
mspc.AddSample(1, sB);
// Act
mspc.Run(new Config(ReplicateType.Biological, 1, 1, 1, 1, 1F, MultipleIntersections.UseLowestPValue));
var cp = mspc.GetConsensusPeaks()[_chr].First();
// Assert
Assert.True(cp.Source.Left == cLeft && cp.Source.Right == cRight);
}
private ReadOnlyDictionary <string, List <ProcessedPeak <Peak> > > GetSampleConsensusPeaks(float alpha = 1e-15F)
{
/// r11 r12
/// Sample 0: ----▓▓▓▓▓▓--------------▓▓▓▓▓▓-----------------------
/// r21 r22 r23 r24
/// Sample 1: --▓▓▓▓▓▓--------▓▓▓-------------░░░---▓▓▓▓▓----------
/// r31 r32 r33
/// Sample 2: -▓▓▓▓▓▓▓▓▓▓▓▓-----------▓▓▓▓▓▓----------▓▓▓▓▓▓▓▓-----
///
var s0 = new Bed <Peak>();
s0.Add(new Peak(10, 20, 1.23E-8), _chrs[0], _strand);
s0.Add(new Peak(50, 60, 1.56E-80), _chrs[2], _strand);
var s1 = new Bed <Peak>();
s1.Add(new Peak(6, 16, 4.56E-8), _chrs[0], _strand);
s1.Add(new Peak(36, 40, 1.31E-23), _chrs[1], _strand);
s1.Add(new Peak(64, 68, 1.02E-2), _chrs[3], _strand);
s1.Add(new Peak(70, 80, 8.76E-9), _chrs[4], _strand);
var s2 = new Bed <Peak>();
s2.Add(new Peak(2, 26, 7.89E-10), _chrs[0], _strand);
s2.Add(new Peak(50, 60, 9.9E-200), _chrs[2], _strand);
s2.Add(new Peak(76, 90, 1.1E-8), _chrs[4], _strand);
var mspc = new Mspc();
mspc.AddSample(0, s0);
mspc.AddSample(1, s1);
mspc.AddSample(2, s2);
mspc.Run(new Config(ReplicateType.Biological, 1E-4, 1E-6, 1E-6, 1, alpha, MultipleIntersections.UseLowestPValue));
return(mspc.GetConsensusPeaks());
}
private string RunMSPCAndExportResultsWithMultiChr()
{
var s0 = new Bed <Peak>();
for (int i = 0; i < peaks.Count; i++)
{
s0.Add(peaks[i], chrs[i], _strand);
}
var s1 = new Bed <Peak>();
s1.Add(new Peak(800, 900, 1E-2), "chr5", _strand);
var mspc = new Mspc();
mspc.AddSample(0, s0);
mspc.AddSample(1, s1);
mspc.Run(new Config(ReplicateType.Biological, 1e-4, 1e-5, 1e-5, 1, 0.05F, MultipleIntersections.UseLowestPValue));
var path = Environment.CurrentDirectory + Path.DirectorySeparatorChar + "MSPCTests_" + new Random().NextDouble().ToString();
new Exporter <Peak>().Export(_sidfm, mspc.GetResults(), mspc.GetConsensusPeaks(), new Options(path, false, _attributes));
return(path);
}
public void RunAsyncIfAtLeastTwoInputIsGiven(int inputCount)
{
// Arrange
var mspc = new Mspc();
if (inputCount == 1)
{
mspc.AddSample(0, new Bed <Peak>());
}
var config = new Config(ReplicateType.Biological, 1e-1, 1e-2, 1e-2, 2, 0.05F, MultipleIntersections.UseLowestPValue);
// Act & Assert
var exception = Assert.Throws <InvalidOperationException>(() => mspc.RunAsync(config));
Assert.Equal(string.Format("Minimum two samples are required; {0} is given.", inputCount), exception.Message);
}
public void AssertCRequirement(int samplesCount, int c, int confirmedPeaksCount, int discardedPeaksCount)
{
// Arrange
uint id = 0;
var mspc = new Mspc();
foreach (var peak in GetPeaks(samplesCount))
{
var sample = new Bed <Peak>();
sample.Add(peak, _chr, _strand);
mspc.AddSample(id++, sample);
}
// Act
var res = mspc.Run(new Config(ReplicateType.Biological, 1e-4, 1e-8, 1e-8, c, 1F, MultipleIntersections.UseLowestPValue));
// Assert
Assert.True(res[0].Chromosomes[_chr].Get(Attributes.Confirmed).Count() == confirmedPeaksCount);
Assert.True(res[0].Chromosomes[_chr].Get(Attributes.Discarded).Count() == discardedPeaksCount);
}
private ReadOnlyDictionary <uint, Result <Peak> > RunThenCancelMSPC(int iCount, Status status)
{
var sA = new Bed <Peak>();
var sB = new Bed <Peak>();
for (int i = 0; i < iCount; i++)
{
sA.Add(new Peak(
left: (10 * i) + 1,
right: (10 * i) + 4,
value: 1E-4,
summit: 0,
name: "r1" + i),
_chr, _strand);
sB.Add(new Peak(
left: (10 * i) + 6,
right: (10 * i) + 9,
value: 1E-5,
summit: 0,
name: "r1" + i),
_chr, _strand);
}
var mspc = new Mspc();
mspc.AddSample(0, sA);
mspc.AddSample(1, sB);
var config = new Config(ReplicateType.Biological, 1e-1, 1e-2, 1e-2, 1, 0.05F, MultipleIntersections.UseLowestPValue);
switch (status)
{
case Status.Init:
_continueIni = new AutoResetEvent(false);
_continueIni.Reset();
mspc.StatusChanged += WaitingIni;
// MSPC is expected to confirm peaks using the following configuration.
mspc.RunAsync(config);
_continueIni.WaitOne();
break;
case Status.Process:
_continuePrc = new AutoResetEvent(false);
_continuePrc.Reset();
mspc.StatusChanged += WaitingPrc;
// MSPC is expected to confirm peaks using the following configuration.
mspc.RunAsync(config);
_continuePrc.WaitOne();
break;
case Status.MTC:
_continueMtc = new AutoResetEvent(false);
_continueMtc.Reset();
mspc.StatusChanged += WaitingMtc;
// MSPC is expected to confirm peaks using the following configuration.
mspc.RunAsync(config);
_continueMtc.WaitOne();
break;
case Status.Consensu:
_continueCon = new AutoResetEvent(false);
_continueCon.Reset();
mspc.StatusChanged += WaitingCon;
// MSPC is expected to confirm peaks using the following configuration.
mspc.RunAsync(config);
_continueCon.WaitOne();
break;
}
// With the following configuration, MSPC discards all the peaks.
// This can help asserting if the asynchronous process of
// the previous execution is canceled, and instead the following asynchronous
// execution is completed.
mspc.RunAsync(new Config(ReplicateType.Biological, 1e-10, 1e-20, 1e-200, 1, 0.05F, MultipleIntersections.UseLowestPValue));
mspc.Done.WaitOne();
return(mspc.GetResults());
}