public FisherExactTestResult Test(PileupItem item, PairedEvent paired)
{
var result = new FisherExactTestResult();
result.Sample1.Name = PositionType.MIDDLE.ToString();
result.Sample2.Name = "TERMINAL";
result.SucceedName = paired.MajorEvent;
result.FailedName = paired.MinorEvent;
foreach (var s in item.Samples)
{
foreach (var b in s)
{
var sample = b.Position == PositionType.MIDDLE ? result.Sample1 : result.Sample2;
if (b.Event.Equals(result.SucceedName))
{
sample.Succeed++;
}
else
{
sample.Failed++;
}
}
}
result.CalculateTwoTailPValue();
return(result);
}
public FisherExactTestResult Test(PileupItem item, PairedEvent paired)
{
var result = new FisherExactTestResult();
result.Sample1.Name = StrandType.FORWARD.ToString();
result.Sample2.Name = StrandType.REVERSE.ToString();
result.SucceedName = paired.MajorEvent;
result.FailedName = paired.MinorEvent;
foreach (var s in item.Samples)
{
foreach (var b in s)
{
var sample = b.Strand == StrandType.FORWARD ? result.Sample1 : result.Sample2;
if (b.Event.Equals(result.SucceedName))
{
sample.Succeed++;
}
else
{
sample.Failed++;
}
}
}
result.CalculateTwoTailPValue();
return(result);
}
public static void PrepareCount(FisherExactTestResult.Sample sample, PairedEvent events, PileupBaseList bases)
{
foreach (var b in bases)
{
if (b.Event.Equals(events.MajorEvent))
{
sample.Succeed++;
}
else if (b.Event.Equals(events.MinorEvent))
{
sample.Failed++;
}
}
}
public FisherExactTestResult InitializeTable(PairedEvent events)
{
var result = new FisherExactTestResult
{
Sample1 = { Name = Samples[0].SampleName },
Sample2 = { Name = Samples[1].SampleName },
SucceedName = events.MajorEvent,
FailedName = events.MinorEvent
};
PrepareCount(result.Sample1, events, _samples[0]);
PrepareCount(result.Sample2, events, _samples[1]);
return(result);
}
public static void PrepareCount(FisherExactTestResult.Sample sample, PairedEvent events, PileupBaseList bases)
{
foreach (var b in bases)
{
if (b.Event.Equals(events.MajorEvent))
{
sample.Succeed++;
}
else if (b.Event.Equals(events.MinorEvent))
{
sample.Failed++;
}
}
}
public FisherExactTestResult InitializeTable(PairedEvent events)
{
var result = new FisherExactTestResult
{
Sample1 = { Name = Samples[0].SampleName },
Sample2 = { Name = Samples[1].SampleName },
SucceedName = events.MajorEvent,
FailedName = events.MinorEvent
};
PrepareCount(result.Sample1, events, _samples[0]);
PrepareCount(result.Sample2, events, _samples[1]);
return result;
}
