//gene enrichment analysis for both Basic PECA and PECA-N
public static IMatrixData GetGOEnr(IMatrixData mdata, string workingDir, int option)//, out string errString)
{
char separator = '\t';
string filename = Path.Combine(workingDir, @".\Goterms.txt");
IMatrixData mNew = (IMatrixData)mdata.CreateNewInstance();
string name = "GSA";
if (option == 0)
{
name = name + "_Degradation";
}
else if (option == 1)
{
name = name + "_Synthesis";
}
mNew.Clear();
mNew.Name = name;
mNew.AltName = name;
//update
//mNew.AltName = "Gene Set Enrichment Analysis";
//mNew.Description = "Gene Set Enrichment Analysis";
string[] colNames = TabSep.GetColumnNames(filename, 0, PerseusUtils.commentPrefix,
PerseusUtils.commentPrefixExceptions, null, separator);
string[][] cols = TabSep.GetColumns(colNames, filename, 0, PerseusUtils.commentPrefix,
PerseusUtils.commentPrefixExceptions, separator);
int nrows = TabSep.GetRowCount(filename);
mNew.Values.Init(nrows, 0);
mNew.SetAnnotationColumns(new List <string>(colNames), new List <string>(colNames), new List <string[]>(cols), new List <string>(),
new List <string>(), new List <string[][]>(), new List <string>(), new List <string>(), new List <double[]>(),
new List <string>(), new List <string>(), new List <double[][]>());
//convert the ones not matching regex to numeric
string pattern = @"^((?!id|name|members).)*$";
Regex numericReg = new Regex(pattern);
List <int> numericList = new List <int>();
for (int i = 0; i < colNames.Length; i++)
{
if (numericReg.Match(colNames[i]).Success)
{
numericList.Add(i);
}
}
StringToNumerical(numericList, mNew);
return(mNew);
}
private static void LoadSplit(IMatrixData mdata, string filename, bool csv)
{
char separator = csv ? ',' : '\t';
string[] colNames = TabSep.GetColumnNames(filename, 0, PerseusUtils.commentPrefix,
PerseusUtils.commentPrefixExceptions, null, separator);
string[][] cols = TabSep.GetColumns(colNames, filename, 0, PerseusUtils.commentPrefix,
PerseusUtils.commentPrefixExceptions, separator);
int nrows = TabSep.GetRowCount(filename);
mdata.Values.Init(nrows, 0);
mdata.SetAnnotationColumns(new List <string>(colNames), new List <string>(colNames), new List <string[]>(cols), new List <string>(),
new List <string>(), new List <string[][]>(), new List <string>(), new List <string>(), new List <double[]>(),
new List <string>(), new List <string>(), new List <double[][]>());
mdata.Origin = filename;
}
//this function is modified from PerseusPluginLib/Load/UnstructuredTxtUpload.cs LoadSplit function
//obtains the output from fdr.exe (so only applicable to PECA CORE and N)
public static void GetOutput(IMatrixData mdata, Parameters param, Parameters dataParam, string filename, string geneName, string expSeries1 = "Expression Series 1", int numOfSeries = 2)
{
char separator = '\t';
//gene name column name is not included in the file so need to replace it
//gene name
ReplaceFirstLine(filename, geneName);
string[] colNames = TabSep.GetColumnNames(filename, 0, PerseusUtils.commentPrefix,
PerseusUtils.commentPrefixExceptions, null, separator);
string[][] cols = TabSep.GetColumns(colNames, filename, 0, PerseusUtils.commentPrefix,
PerseusUtils.commentPrefixExceptions, separator);
int nrows = TabSep.GetRowCount(filename);
string[] expressionColumnsNames = ArrayUtils.Concat(mdata.ColumnNames, mdata.NumericColumnNames);
mdata.Clear();
mdata.Name = "PECA Analysis";
mdata.Values.Init(nrows, 0);
mdata.SetAnnotationColumns(new List <string>(colNames), new List <string>(colNames), new List <string[]>(cols), new List <string>(),
new List <string>(), new List <string[][]>(), new List <string>(), new List <string>(), new List <double[]>(),
new List <string>(), new List <string>(), new List <double[][]>());
//be careful with changes of Number of time points in the future
int numOfExpCols = numOfSeries * dataParam.GetParam <int[]>(expSeries1).Value.Length;
//file format is structured so that expressions columns are before numeric ones
//so convert the numeric ones before expression columns
//first column guaranteed to be the name column
int[] expList = Enumerable.Range(1, numOfExpCols).ToArray();
int[] numericList = Enumerable.Range(numOfExpCols + 1, colNames.Count() - numOfExpCols - 1).ToArray();
StringToNumerical(numericList, mdata);
StringToExpression(expList, mdata);
}
