public QuantMethods(Replicate replicate, Master master, SQLiteConnection quantDbConnection)
{
CurrentReplicate = replicate;
Master = master;
ReplicateDBConnection = new SQLiteConnection(@"Data Source=" + replicate.gcFeatFilePath);
ReplicateDBConnection.Open();
QuantDbConnection = quantDbConnection;
}
public static void NormalizeRepToRefExperimentLinear(Batch referenceBatch, Replicate rep)
{
List <Tuple <double, double, int> > bothVals = new List <Tuple <double, double, int> >();
foreach (var key in rep.quantDictionary.Keys)
{
var lfqOne = referenceBatch.avgQuantDict[key].AvgIntensity;
var lfqTwo = rep.quantDictionary[key].ApexIntensity_Normalized;
//calculate m
var m = (lfqOne / lfqTwo);
m = Math.Log(m, 2);
//calculate a
var a = (lfqTwo * lfqOne);
a = Math.Log(a, 2);
a /= 2;
bothVals.Add(new Tuple <double, double, int>(a, m, key));
}
List <double> xVals = new List <double>();
List <double> yVals = new List <double>();
foreach (var val in bothVals)
{
xVals.Add(val.Item1);
yVals.Add(val.Item2);
}
double slope;
double yIntercept;
double rSquared;
Statistics.LinearRegression(xVals.ToArray(), yVals.ToArray(), 0, xVals.Count(), out rSquared, out yIntercept, out slope);
foreach (var key in rep.quantDictionary.Keys)
{
var lfqOne = referenceBatch.avgQuantDict[key].AvgIntensity;
var lfqTwo = rep.quantDictionary[key].ApexIntensity_Normalized;
//calculate m
var m = (lfqOne / lfqTwo);
m = Math.Log(m, 2);
//calculate a
var a = (lfqTwo * lfqOne);
a = Math.Log(a, 2);
a /= 2;
//get predicted mi-star from
var mistar = (a * slope) + yIntercept;
var corrFactor = m - mistar;
rep.quantDictionary[key].ApexIntensity_Normalized = Math.Pow(2, -(corrFactor - (2 * a)) / 2);
rep.quantDictionary[key].ApexIntensity = Math.Pow(2, -(corrFactor - (2 * a)) / 2);
}
}
public static void NormalizeRepToReferenceExperiment(Batch referenceBatch, Replicate rep)
{
List <Tuple <double, double, int> > bothVals = new List <Tuple <double, double, int> >();
foreach (var key in rep.quantDictionary.Keys)
{
var lfqOne = referenceBatch.avgQuantDict[key].AvgIntensity;
var lfqTwo = rep.quantDictionary[key].ApexIntensity_Normalized;
//calculate m
var m = (lfqOne / lfqTwo);
m = Math.Log(m, 2);
//calculate a
var a = (lfqTwo * lfqOne);
a = Math.Log(a, 2);
a /= 2;
bothVals.Add(new Tuple <double, double, int>(a, m, key));
}
List <double> xVals = new List <double>();
List <double> yVals = new List <double>();
var li = new LowessInterpolator(.4, 0);
bothVals = bothVals.OrderBy(t => t.Item1).ToList();
foreach (var val in bothVals)
{
xVals.Add(val.Item1);
yVals.Add(val.Item2);
}
var smoothed = li.smooth(xVals.ToArray(), yVals.ToArray());
for (int q = 0; q < smoothed.Length; q++)
{
var residual = smoothed[q];
var key = bothVals[q].Item3;
var lfqOne = referenceBatch.avgQuantDict[key].AvgIntensity;
var lfqTwo = rep.quantDictionary[key].ApexIntensity_Normalized;
//calculate m
var m = (lfqOne / lfqTwo);
m = Math.Log(m, 2);
//calculate a
var a = (lfqTwo * lfqOne);
a = Math.Log(a, 2);
a /= 2;
var corrFactor = -residual;
//repAQuantDict[key].NormalizedIntensity = Math.Pow(2, (corrFactor + (2 * a)) / 2);
rep.quantDictionary[key].ApexIntensity_Normalized = Math.Pow(2, -(corrFactor - (2 * a)) / 2);
rep.quantDictionary[key].ApexIntensity = Math.Pow(2, -(corrFactor - (2 * a)) / 2);
}
}
public static Dictionary <int, Batch> GetBatchDictionary(SQLiteConnection conn)
{
Dictionary <int, Batch> batchDict = new Dictionary <int, Batch>();
var queryText = "SELECT s.Name, s.Batch_ID FROM Batch_Table s";
var command = new SQLiteCommand(queryText, conn);
var reader = command.ExecuteReader();
while (reader.Read())
{
var name = reader["Name"].ToString();
var id = int.Parse(reader["Batch_ID"].ToString());
var newBatch = new Batch();
newBatch.batchID = id;
newBatch.name = name;
batchDict.Add(id, newBatch);
}
reader.Close();
queryText = "SELECT s.Name, s.Replicate_ID, s.GCFeatPath, s.BatchName, s.Batch_ID, s.ControlBatchName, s.ControlBatch_ID FROM Replicate_Table s";
command = new SQLiteCommand(queryText, conn);
reader = command.ExecuteReader();
while (reader.Read())
{
var name = reader["Name"].ToString();
var id = int.Parse(reader["Replicate_ID"].ToString());
var path = reader["GCFeatPath"].ToString();
var batchName = reader["BatchName"].ToString();
var batchID = int.Parse(reader["Batch_ID"].ToString());
var controlName = reader["ControlBatchName"].ToString();
var controlID = reader["ControlBatch_ID"].ToString();
var newRep = new Replicate();
newRep.batchID = batchID;
newRep.batchName = batchName;
newRep.gcFeatFilePath = path;
newRep.name = name;
newRep.replicateID = id;
var currBatch = batchDict[batchID];
currBatch.replicates.Add(newRep);
if (!string.IsNullOrEmpty(controlID))
{
var control_ID = int.Parse(controlID);
//var currBatch = batchDict[batchID];
//currBatch.replicates.Add(newRep);
newRep.controlName = controlName;
newRep.control = batchDict[control_ID];
currBatch.control = batchDict[control_ID];
currBatch.controlID = control_ID;
}
}
return(batchDict);
}
public void CreateBatchDictionary()
{
BatchDictionary = new Dictionary <string, Batch>();
var gcExpReader = new StreamReader(gcExpTextBox.Text);
HashSet <string> batchNamesHashSet = new HashSet <string>();
List <Replicate> replicates = new List <Replicate>();
List <Batch> batches = new List <Batch>();
while (gcExpReader.Peek() > -1)
{
var currLine = gcExpReader.ReadLine();
if (!currLine.Equals("\t\t\t\t") && !string.IsNullOrEmpty(currLine))
{
string[] parts = currLine.Split('\t');
var gcFeatPath = parts[0];
var name = parts[1];
var batchName = parts[2];
var controlBatchName = parts[3];
if (string.IsNullOrEmpty(batchName))
{
batchName = name;
}
var newRep = new Replicate();
newRep.name = name;
newRep.gcFeatFilePath = gcFeatPath;
batchNamesHashSet.Add(batchName);
batchNamesHashSet.Add(controlBatchName);
newRep.controlName = controlBatchName;
newRep.batchName = batchName;
replicates.Add(newRep);
}
}
foreach (var batch in batchNamesHashSet.ToList())
{
var newBatch = new Batch();
newBatch.name = batch;
batches.Add(newBatch);
BatchDictionary.Add(newBatch.name, newBatch);
}
foreach (var rep in replicates)
{
var currBatch = BatchDictionary[rep.batchName];
currBatch.replicates.Add(rep);
rep.control = BatchDictionary[rep.controlName];
}
foreach (var batch in BatchDictionary.Where(x => x.Value.replicates.Count == 0).ToList())
{
BatchDictionary.Remove(batch.Key);
}
ReplicateList = new List <Replicate>();
foreach (var batch in BatchDictionary.Values)
{
foreach (var rep in batch.replicates)
{
if (!BatchDictionary.ContainsKey(rep.controlName))
{
rep.control = null;
rep.controlName = null;
}
ReplicateList.Add(rep);
}
}
}
