public void ReferenceCopyNumberByPloidy_IsExcluded()
{
var calculator = new CopyNumberBedGraphCalculator();
var segments = new List <CanvasSegment>
{
new CanvasSegment("chrX", 0, 1, new List <SampleGenomicBin>
{
new SampleGenomicBin("chrX", 0, 1, 3f)
})
{
CopyNumber = 1,
MajorChromosomeCount = 1,
Filter = CanvasFilter.PassFilter
}
};
var ploidyInfo = new PloidyInfo {
PloidyByChromosome = ("chrX", new PloidyInterval("chr1")
{
Start = 0, End = 1, Ploidy = 1
}.Yield().ToList()).Yield().ToDictionary()
};
var results = calculator.Calculate(segments, ploidyInfo).ToList();
Assert.Empty(results);
}
public void NoSegments_ReturnsNoBedGraphEntries()
{
var calculator = new CopyNumberBedGraphCalculator();
var segments = Enumerable.Empty <CanvasSegment>().ToList();
var ploidyInfo = new PloidyInfo();
var results = calculator.Calculate(segments, ploidyInfo);
Assert.Empty(results);
}
public void ReferenceCopyNumber_IsExcluded()
{
var calculator = new CopyNumberBedGraphCalculator();
var segments = new List <CanvasSegment>
{
new CanvasSegment("chr1", 0, 1, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 0, 1, 3f)
})
{
CopyNumber = 2,
Filter = CanvasFilter.PassFilter
}
};
var ploidyInfo = new PloidyInfo();
var results = calculator.Calculate(segments, ploidyInfo).ToList();
Assert.Empty(results);
}
public void FiltersNonPassSegments()
{
var calculator = new CopyNumberBedGraphCalculator();
var segments = new List <CanvasSegment>
{
new CanvasSegment("chr1", 0, 1, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 0, 1, 3f)
})
{
CopyNumber = 0,
Filter = CanvasFilter.Create("NonPass".Yield())
}
};
var ploidyInfo = new PloidyInfo();
var results = calculator.Calculate(segments, ploidyInfo);
Assert.Empty(results);
}
public void LOH_IsIncluded()
{
var calculator = new CopyNumberBedGraphCalculator();
var segments = new List <CanvasSegment>
{
new CanvasSegment("chr1", 0, 1, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 0, 1, 3f)
})
{
CopyNumber = 2,
MajorChromosomeCount = 2,
Filter = CanvasFilter.PassFilter
}
};
var ploidyInfo = new PloidyInfo();
var results = calculator.Calculate(segments, ploidyInfo).ToList();
Assert.Equal(2m, results.First().Value);
}
public void VariantCopyNumber_ReturnsCopyNumber()
{
var calculator = new CopyNumberBedGraphCalculator();
var segments = new List <CanvasSegment>
{
new CanvasSegment("chr1", 0, 1, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 0, 1, 3f)
})
{
CopyNumber = 1,
Filter = CanvasFilter.PassFilter
}
};
var ploidyInfo = new PloidyInfo();
var results = calculator.Calculate(segments, ploidyInfo).ToList();
Assert.Equal("chr1", results.First().Chromosome);
Assert.Equal(new BedInterval(0, 1), results.First().Interval);
Assert.Equal(1m, results.First().Value);
}
