static void Main(string[] args)
{
System.Console.WriteLine("Welcome to the Kaplan-Meier estimator program!");
SetParams();
var patientReader = new ExcelPatientReader(Path.Combine(Directory.GetCurrentDirectory(), PatientFileName), PatientSheetName, hasHeader: true);
patientReader.RegisterParser(@"Patientnummer", (value, patient) => patient.Id = int.Parse(value));
patientReader.RegisterParser(@"EventFreeSurvival_event (metastasis or death)", (value, patient) => patient.CensorEvent = (EventFreeSurvival)Enum.Parse(typeof(EventFreeSurvival), value));
patientReader.RegisterParser(@"reg_t_fu_months", (value, patient) => patient.CensorEventTime = (int)Math.Floor(double.Parse(value)));
var geneReader = new CSVGeneReader(Path.Combine(Directory.GetCurrentDirectory(), GeneFileName));
var patients = patientReader.ReadToEnd().ToDictionary(patient => patient.Id);
var genes = geneReader.GetGenes().ToList();
ISplitStrategy[] splitStrategies = null;
if (Time == "before")
{
splitStrategies = new ISplitStrategy[] { new T0_TopNPercentSplitStrategy(Percentile, patients) };
}
if (Time == "after")
{
splitStrategies = new ISplitStrategy[] { new T2_TopNPercentSplitStrategy(Percentile, patients) };
}
if (Time == "diff")
{
splitStrategies = new ISplitStrategy[] { new T0T2Diff_TopNPercentSplitStrategy(Percentile, patients) };
}
string currentDir = Directory.GetCurrentDirectory();
foreach (var strategy in splitStrategies)
{
if (Directory.Exists(Path.Combine(currentDir, strategy.Name)))
{
Directory.Delete(Path.Combine(currentDir, strategy.Name), true);
}
DirectoryInfo targetDir = Directory.CreateDirectory(Path.Combine(currentDir, strategy.Name));
if (!targetDir.Exists)
{
targetDir.Create();
}
StrategyRunner runner = new StrategyRunner(strategy);
var orderedResults = runner.Run(genes).ToArray();
int resultsCount = orderedResults.Length;
for (int index = 0; index < resultsCount; index++)
{
var result = orderedResults[index];
result.FDR = (result.Estimate.PValue * resultsCount) / (index + 1);
}
File.WriteAllText(Path.Combine(targetDir.FullName, "Results.csv"), "Illumina ID, P-Value, -Log(P-Value), FDR, GroupSize" + Environment.NewLine);
File.AppendAllLines(Path.Combine(targetDir.FullName, "Results.csv"), orderedResults.Select((result, index) => string.Format("{0}, {1:E}, {2}, {3}, {4}", result.GeneId, result.Estimate.PValue, -Math.Log10(result.Estimate.PValue), (result.Estimate.PValue * resultsCount) / (index + 1), result.GroupSize)));
var logRankDir = targetDir.CreateSubdirectory("Results_LogRank");
ExcelWritter excelOutput = new ExcelWritter(logRankDir, orderedResults, result => - Math.Log10(result.Estimate.PValue));
excelOutput.WriteExcelFiles();
orderedResults = orderedResults.OrderBy(result => result.FDR).ToArray();
var fdrRankDir = targetDir.CreateSubdirectory("Results_FDR");
excelOutput = new ExcelWritter(fdrRankDir, orderedResults, result => result.FDR);
excelOutput.WriteExcelFiles();
System.Console.WriteLine("Output is ready at {0}", targetDir.FullName);
System.Console.ReadLine();
}
}
static void Main2(string[] args)
{
var groupA = new List <Patient>
{
new Patient {
CensorEventTime = 2, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 3, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 5, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 5, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 5, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 5, CensorEvent = EventFreeSurvival.Censored
},
new Patient {
CensorEventTime = 8, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 8, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 8, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 9, CensorEvent = EventFreeSurvival.Censored
},
new Patient {
CensorEventTime = 10, CensorEvent = EventFreeSurvival.Censored
},
new Patient {
CensorEventTime = 10, CensorEvent = EventFreeSurvival.Censored
},
new Patient {
CensorEventTime = 11, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 11, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 12, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 12, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 13, CensorEvent = EventFreeSurvival.Censored
},
new Patient {
CensorEventTime = 13, CensorEvent = EventFreeSurvival.Censored
},
};
var groupB = new List <Patient>
{
new Patient {
CensorEventTime = 1, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 3, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 4, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 6, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 6, CensorEvent = EventFreeSurvival.Censored
},
new Patient {
CensorEventTime = 6, CensorEvent = EventFreeSurvival.Censored
},
new Patient {
CensorEventTime = 8, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 8, CensorEvent = EventFreeSurvival.Censored
},
new Patient {
CensorEventTime = 9, CensorEvent = EventFreeSurvival.Censored
},
new Patient {
CensorEventTime = 10, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 10, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 12, CensorEvent = EventFreeSurvival.Censored
},
new Patient {
CensorEventTime = 12, CensorEvent = EventFreeSurvival.Censored
},
new Patient {
CensorEventTime = 13, CensorEvent = EventFreeSurvival.Death
},
new Patient {
CensorEventTime = 13, CensorEvent = EventFreeSurvival.Censored
},
new Patient {
CensorEventTime = 13, CensorEvent = EventFreeSurvival.Censored
},
};
KaplanMeierEstimate estimate = new KaplanMeierEstimate(groupA, groupB);
estimate.RunEstimate();
CSVGeneReader reader = new CSVGeneReader(@"C:\Users\sashaa\Source\Workspaces\KaplanMeierEstimator\SampleFiles\PathologicalDatabaseGenes.csv");
var x = reader.GetGenes();
}