internal void Run(Config config, BackgroundWorker worker, DoWorkEventArgs e)
{
_config = config;
_worker = worker;
_workerEventArgs = e;
int step = 1, stepCount = 4;
OnProgressUpdate(new ProgressReport(step++, stepCount, "Initializing"));
CacheChiSqrdData();
BuildDataStructures();
if (CheckCancellationPending())
{
return;
}
OnProgressUpdate(new ProgressReport(step++, stepCount, "Processing samples"));
ProcessSamples();
if (CheckCancellationPending())
{
return;
}
OnProgressUpdate(new ProgressReport(step++, stepCount, "Performing Multiple testing correction"));
var fdr = new FalseDiscoveryRate <I>();
fdr.PerformMultipleTestingCorrection(_analysisResults, _config.Alpha, DegreeOfParallelism);
if (CheckCancellationPending())
{
return;
}
OnProgressUpdate(new ProgressReport(step, stepCount, "Creating consensus peaks set"));
_consensusPeaks = new ConsensusPeaks <I>().Compute(_analysisResults, _peakConstructor, DegreeOfParallelism, _config.Alpha);
}
public Dictionary <string, List <ProcessedPeak <I> > > Compute(
Dictionary <uint, Result <I> > analysisResults,
IPeakConstructor <I> peakConstructor,
int degreeOfParallelisim,
float alpha)
{
// Initialize data structures.
_consensusPeaks = new Dictionary <string, SortedDictionary <Interval, Interval> >();
foreach (var result in analysisResults)
{
foreach (var chr in result.Value.Chromosomes)
{
if (!_consensusPeaks.ContainsKey(chr.Key))
{
_consensusPeaks.Add(chr.Key, new SortedDictionary <Interval, Interval>());
}
}
}
// Determin consensus peaks; stored in mutable and light-weight types.
foreach (var result in analysisResults)
{
Parallel.ForEach(
result.Value.Chromosomes,
new ParallelOptions {
MaxDegreeOfParallelism = degreeOfParallelisim
},
chr =>
{
DetermineConsensusPeaks(chr.Key, chr.Value.Get(Attributes.Confirmed));
});
}
// Convert the type of determined consensus peaks.
var processedPeaks = ConvertToListOfProcessedPeaks(peakConstructor, degreeOfParallelisim);
var fdr = new FalseDiscoveryRate <I>();
fdr.PerformMultipleTestingCorrection(processedPeaks, alpha);
return(processedPeaks);
}
