public static string Get_complete_sampleName(Entry_type_enum entryType, int timepoint, string sampleName)
{
StringBuilder sb = new StringBuilder();
if (!entryType.Equals(Entry_type_enum.E_m_p_t_y))
{
if (sb.Length > 0)
{
sb.AppendFormat("-");
}
sb.AppendFormat(entryType.ToString());
}
if (!String.IsNullOrEmpty(sampleName))
{
if (sb.Length > 0)
{
sb.AppendFormat("-");
}
sb.AppendFormat(sampleName);
}
if (sb.Length > 0)
{
sb.AppendFormat("-");
}
sb.AppendFormat(timepoint.ToString());
return(sb.ToString());
}
public void Merge_all_columns()
{
int columns_count = this.Columns_length;
Colchar_column_line_class column_line;
StringBuilder sb_new_name = new StringBuilder();
sb_new_name.AppendFormat("Merged");
Entry_type_enum entryType = this.Columns[0].EntryType;
for (int indexC = 0; indexC < columns_count; indexC++)
{
column_line = this.Columns[indexC];
if (!column_line.EntryType.Equals(entryType))
{
throw new Exception();
}
sb_new_name.AppendFormat("-");
sb_new_name.AppendFormat("{0}", column_line.Timepoint);
}
Colchar_column_line_class new_column_line = new Colchar_column_line_class(entryType, 0, sb_new_name.ToString());
this.Columns = new Colchar_column_line_class[] { new_column_line };
}
private Ontology_enrichment_line_class[] Generate_enrichment_lines_and_calculate_pvalues(string[] experimental_symbols, Entry_type_enum entryType, int timepoint, string sample_name)
{
experimental_symbols = experimental_symbols.Distinct().OrderBy(l => l).ToArray();
int experimental_symbols_length = experimental_symbols.Length;
Dictionary <string, int> processName_symbol_count = new Dictionary <string, int>();
Dictionary <string, List <string> > processName_symbol_overlap_symbols = new Dictionary <string, List <string> >();
MBCO_association.Order_by_symbol_processName();
#region Count overlap between process genes and experimental genes
string experimental_symbol;
int mbco_associations_length = MBCO_association.MBCO_associations.Length;
int indexSymbol = 0;
int stringCompare;
MBCO_association_line_class mbco_association_line;
for (int indexMBCO = 0; indexMBCO < mbco_associations_length; indexMBCO++)
{
mbco_association_line = MBCO_association.MBCO_associations[indexMBCO];
stringCompare = -2;
while ((indexSymbol < experimental_symbols_length) && (stringCompare < 0))
{
experimental_symbol = experimental_symbols[indexSymbol];
stringCompare = experimental_symbol.CompareTo(mbco_association_line.Symbol);
if (stringCompare < 0)
{
indexSymbol++;
}
else if (stringCompare == 0)
{
#region Overlap symbols
if (!processName_symbol_overlap_symbols.ContainsKey(mbco_association_line.ProcessName))
{
processName_symbol_overlap_symbols.Add(mbco_association_line.ProcessName, new List <string>());
}
processName_symbol_overlap_symbols[mbco_association_line.ProcessName].Add(experimental_symbol);
#endregion
}
}
#region Process symbol count
if ((indexMBCO != 0) &&
(mbco_association_line.ProcessName.Equals(MBCO_association.MBCO_associations[indexMBCO - 1].ProcessName)) &&
(mbco_association_line.Symbol.Equals(MBCO_association.MBCO_associations[indexMBCO - 1].Symbol)))
{
throw new Exception();
}
if (!processName_symbol_count.ContainsKey(mbco_association_line.ProcessName))
{
processName_symbol_count.Add(mbco_association_line.ProcessName, 1);
}
else
{
processName_symbol_count[mbco_association_line.ProcessName]++;
}
#endregion
}
#endregion
#region Generate enrichment lines
string[] processNames = processName_symbol_overlap_symbols.Keys.ToArray();
string processName;
int processNames_length = processNames.Length;
Ontology_enrichment_line_class[] enrich_lines = new Ontology_enrichment_line_class[processNames_length];
Ontology_enrichment_line_class new_enrich_line;
for (int indexP = 0; indexP < processNames_length; indexP++)
{
processName = processNames[indexP];
new_enrich_line = new Ontology_enrichment_line_class();
new_enrich_line.Ontology_type = this.Ontology;
new_enrich_line.Scp_name = (string)processName.Clone();
new_enrich_line.Experimental_symbols_count = experimental_symbols_length;
new_enrich_line.Process_symbols_count = processName_symbol_count[processName];
new_enrich_line.Bg_symbol_count = this.Bg_genes.Length;
new_enrich_line.Overlap_symbols = processName_symbol_overlap_symbols[processName].OrderBy(l => l).ToArray();
new_enrich_line.Overlap_count = new_enrich_line.Overlap_symbols.Length;
new_enrich_line.EntryType = entryType;
new_enrich_line.Timepoint = timepoint;
new_enrich_line.Sample_name = (string)sample_name.Clone();
enrich_lines[indexP] = new_enrich_line;
}
#endregion
#region Calculate pvalues
int enrich_length = enrich_lines.Length;
Ontology_enrichment_line_class enrich_line;
int a; int b; int c; int d;
Fisher_exact_test_class fisher = new Fisher_exact_test_class(this.Bg_genes.Length, false);
for (int indexE = 0; indexE < enrich_length; indexE++)
{
enrich_line = enrich_lines[indexE];
a = enrich_line.Overlap_count;
b = enrich_line.Experimental_symbols_count - a;
c = enrich_line.Process_symbols_count - a;
d = enrich_line.Bg_symbol_count - a - b - c;
if ((a < 0) || (b < 0) || (c < 0) || (d < 0))
{
throw new Exception("negative values");
}
enrich_line.Pvalue = fisher.Get_rightTailed_p_value(a, b, c, d);
enrich_line.Minus_log10_pvalue = -(float)Math.Log10(enrich_line.Pvalue);
}
#endregion
#region Calculate qvalues and FDR
enrich_lines = enrich_lines.OrderBy(l => l.Pvalue).ToArray();
int enrich_lines_length = enrich_lines.Length;
int rank = 0;
for (int indexE = 0; indexE < enrich_lines_length; indexE++)
{
enrich_line = enrich_lines[indexE];
rank++;
enrich_line.Qvalue = enrich_line.Pvalue * ((double)processNames_length / (double)rank);
if (enrich_line.Qvalue > 1)
{
enrich_line.Qvalue = 1;
}
}
double lowest_qvalue = -1;
for (int indexE = enrich_lines_length - 1; indexE >= 0; indexE--)
{
enrich_line = enrich_lines[indexE];
if ((lowest_qvalue == -1) ||
(lowest_qvalue > enrich_line.Qvalue))
{
lowest_qvalue = enrich_line.Qvalue;
}
enrich_line.FDR = lowest_qvalue;
}
#endregion
return(enrich_lines);
}
public void Get_entryType_timepoint_and_name_of_indicated_column(out Entry_type_enum entryType, out float timepoint, out string name, int indexColumn)
{
entryType = Columns[indexColumn].EntryType;
timepoint = Columns[indexColumn].Timepoint;
name = (string)Columns[indexColumn].SampleName.Clone();
}
public Colchar_column_line_class(Entry_type_enum entryType, int timepoint, string sampleName)
{
this.EntryType = entryType;
this.Timepoint = timepoint;
SampleName = (string)sampleName.Clone();
}
