public double Get_leftTailed_p_value(int a, int b, int c, int d)
{
if (Report)
{
Report_class.WriteLine("{0}: Get left tailed p-value", typeof(Fisher_exact_test_class).Name);
}
double p;
if (Check_if_n_not_larger_than_max_size(a, b, c, d))
{
p = Get_specific_p_value(a, b, c, d);
int min = (a < d) ? a : d;
for (int i = 0; i < min; i++)
{
p += Get_specific_p_value(--a, ++b, ++c, --d);
}
}
else
{
p = -1;
};
if (Report)
{
for (int i = 0; i < typeof(Fisher_exact_test_class).Name.Length + 2; i++)
{
Report_class.Write(" ");
}
Report_class.WriteLine("p_value: {0}", p);
}
if (p > 1)
{
p = 1;
}
return(p);
}
public static void Delete_files_in_directory_that_start_with_startString(string directory, string startString)
{
string[] complete_file_names = Directory.GetFiles(directory);
int complete_file_names_length = complete_file_names.Length;
if (complete_file_names_length > 0)
{
Report_class.Write("Delete files in directory {0}:", directory);
Console.ReadLine();
string[] file_names = new string[complete_file_names_length];
for (int indexC = 0; indexC < complete_file_names_length; indexC++)
{
file_names[indexC] = Path.GetFileName(complete_file_names[indexC]);
}
foreach (string file_name in file_names)
{
if (file_name.IndexOf(startString) == 0)
{
FileInfo delete_file = new FileInfo(directory + file_name);
delete_file.Delete();
}
}
}
}
public double Get_rightTailed_p_value(int a, int b, int c, int d)
{
if (Report)
{
Report_class.WriteLine("{0}: Get right tailed p-value", typeof(Fisher_exact_test_class).Name);
}
double p;
if (Check_if_n_not_larger_than_max_size(a, b, c, d))
{
p = Get_specific_p_value(a, b, c, d);
int min = (c < b) ? c : b;
for (int i = 0; i < min; i++)
{
p += Get_specific_p_value(++a, --b, --c, ++d);
}
}
else
{
p = -1;
};
if (Report)
{
for (int i = 0; i < typeof(Fisher_exact_test_class).Name.Length + 2; i++)
{
Report_class.Write(" ");
}
Report_class.WriteLine("p_value: {0}", p);
}
return(p);
}
public static void Delete_directory_if_it_exists(string directory)
{
if (Directory.Exists(directory))
{
Report_class.Write("Delete {0}?", directory);
Console.Read();
Directory.Delete(directory, true);
}
}
public static void Delete_file_if_it_exists(string complete_file_name)
{
if (File.Exists(complete_file_name))
{
Report_class.Write("Delete file: {0}?", complete_file_name);
Console.ReadLine();
FileInfo delete_file = new FileInfo(complete_file_name);
delete_file.Delete();
Report_class.WriteLine(" deleted");
}
}
public static void Delete_files_in_directory(string directory)
{
string[] complete_file_names = Directory.GetFiles(directory);
if (complete_file_names.Length > 0)
{
Report_class.Write("Delete files in directory {0}:", directory);
Console.ReadLine();
foreach (string complete_file_name in complete_file_names)
{
FileInfo delete_file = new FileInfo(complete_file_name);
delete_file.Delete();
}
}
}
private void Print_options()
{
Report_class.WriteLine("{0}: Print options", typeof(Ontology_process_analysis_options_class).Name);
for (int i = 0; i < typeof(Ontology_process_analysis_options_class).Name.Length + 2; i++)
{
Report_class.Write(" ");
}
Report_class.Write("Used Ontologies:");
for (int i = 0; i < Ontologies.Length; i++)
{
Report_class.Write(" {0}", Ontologies[i]);
}
Report_class.WriteLine();
}
public static void Delete_file_if_it_exists(string complete_file_name)
{
Report_class.Write("Delete file {0}:", complete_file_name);
if (File.Exists(complete_file_name))
{
FileInfo delete_file = new FileInfo(complete_file_name);
delete_file.Delete();
Report_class.WriteLine(" deleted");
}
else
{
Report_class.WriteLine(" File does not exist");
}
}
public void Print_options()
{
Report_class.WriteLine("{0}: Print options", typeof(Mbc_enrichment_pipeline_options_class).Name);
int right_shift = 4;
#region Write general options
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.WriteLine("General:");
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.WriteLine("Report: {0}", Report);
Report_class.WriteLine();
#endregion
#region Write parameter for both standard and dynamic enrichment analysis
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.WriteLine("Parameter for both standard and dynamic enrichment analysis:");
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.Write("Data value signs of interest:");
int signs_of_interest_length = Data_value_signs_of_interest.Length;
for (int indexS = 0; indexS < signs_of_interest_length; indexS++)
{
if (indexS != 0)
{
Report_class.Write(",");
}
Report_class.Write(" {0}", Data_value_signs_of_interest[indexS]);
}
Report_class.WriteLine();
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.WriteLine("Maximum pvalue: {0}", Maximum_pvalue_for_standardDynamicEnrichment);
Report_class.WriteLine();
#endregion
#region Write parameter for standard enrichment analysis
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.WriteLine("Parameter for standard enrichment analysis only:");
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.Write("Keep top predictions:");
int keep_top_length = Kept_top_predictions_standardEnrichment_per_level.Length;
for (int level = 1; level < keep_top_length; level++)
{
if (level != 1)
{
Report_class.Write(", ");
}
Report_class.Write(" Level {0}: {1}", level, Kept_top_predictions_standardEnrichment_per_level[level]);
}
Report_class.WriteLine();
Report_class.WriteLine();
#endregion
#region Write parameter for dyanmic enrichment analysis
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.WriteLine("Parameter for dynamic enrichment analysis only:");
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.Write("Do dynamic enrichment for: ");
int scp_levels_for_dynamicEnrichment_length = Scp_levels_for_dynamicEnrichment.Length;
for (int indexLevel = 0; indexLevel < scp_levels_for_dynamicEnrichment_length; indexLevel++)
{
if ((indexLevel != 0) && (indexLevel == scp_levels_for_dynamicEnrichment_length - 1))
{
Report_class.Write(" and ");
}
else if (indexLevel != 0)
{
Report_class.Write(", ");
}
Report_class.Write(" Level {0}", Scp_levels_for_dynamicEnrichment[indexLevel]);
}
Report_class.WriteLine();
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.WriteLine("Number of neighboring SCPs that are merged to SCP unions:");
for (int indexLevel = 0; indexLevel < scp_levels_for_dynamicEnrichment_length; indexLevel++)
{
int level = Scp_levels_for_dynamicEnrichment[indexLevel];
int[] merge_scps_current_level = Numbers_of_merged_scps_for_dynamicEnrichment_per_level[level];
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.Write("To generate level-{0} SCP unions merge ", level);
int merge_length = merge_scps_current_level.Length;
for (int indexM = 0; indexM < merge_length; indexM++)
{
if ((indexM != 0) && (indexM == merge_length - 1))
{
Report_class.Write(" or ");
}
else if (indexM != 0)
{
Report_class.Write(", ");
}
Report_class.Write("{0}", merge_scps_current_level[indexM]);
}
Report_class.WriteLine(" SCPs");
}
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.Write("Top quantile of scp interactions that are considered to identify neighboring SCPs: ");
int top_quantile_length = Top_quantile_of_scp_interactions_for_dynamicEnrichment_per_level.Length;
for (int indexLevel = 0; indexLevel < scp_levels_for_dynamicEnrichment_length; indexLevel++)
{
int level = Scp_levels_for_dynamicEnrichment[indexLevel];
if (indexLevel != 0)
{
Report_class.Write(", ");
}
Report_class.WriteLine("Level {0}: {1}", level, Top_quantile_of_scp_interactions_for_dynamicEnrichment_per_level[level]);
}
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.Write("Top quantile of scp interactions that are considered to visualize SCP network:");
top_quantile_length = Top_quantile_of_scp_interactions_for_visualization_of_dynamicEnrichment_per_level.Length;
for (int indexLevel = 0; indexLevel < scp_levels_for_dynamicEnrichment_length; indexLevel++)
{
int level = Scp_levels_for_dynamicEnrichment[indexLevel];
if (indexLevel != 1)
{
Report_class.Write(", ");
}
Report_class.Write("Level {0}: {1}", level, Top_quantile_of_scp_interactions_for_visualization_of_dynamicEnrichment_per_level[level]);
}
Report_class.WriteLine();
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.Write("Keep top predicted SCP unions or single SCPs: ");
top_quantile_length = Top_quantile_of_scp_interactions_for_visualization_of_dynamicEnrichment_per_level.Length;
for (int indexLevel = 0; indexLevel < scp_levels_for_dynamicEnrichment_length; indexLevel++)
{
int level = Scp_levels_for_dynamicEnrichment[indexLevel];
if (indexLevel != 0)
{
Report_class.Write(", ");
}
Report_class.Write("Level {0}: {1}", level, Kept_top_predictions_dynamicEnrichment_per_level[level]);
}
Report_class.WriteLine();
for (int i = 0; i < right_shift; i++)
{
Report_class.Write(" ");
}
Report_class.Write("Keep not more than x SCPs as part of a single SCP prediction or a predicted SCP-union: ");
top_quantile_length = Top_quantile_of_scp_interactions_for_visualization_of_dynamicEnrichment_per_level.Length;
for (int indexLevel = 0; indexLevel < scp_levels_for_dynamicEnrichment_length; indexLevel++)
{
int level = Scp_levels_for_dynamicEnrichment[indexLevel];
if (indexLevel != 0)
{
Report_class.Write(", ");
}
Report_class.WriteLine("Level {0}: {1}", level, Kept_singleSCPs_dynamicEnrichment_per_level[level]);
}
Report_class.WriteLine();
#endregion
}
