public Ontology_enrichment_class Analyse_data_instance(Data_class data_input)
{
Data_class data = data_input.Deep_copy();
data.Keep_only_input_rowNames(this.Bg_genes);
int data_length = data.Data_length;
int col_length = data.ColChar.Columns_length;
string[] symbols;
List <Ontology_enrichment_line_class> enrich_list = new List <Ontology_enrichment_line_class>();
Ontology_enrichment_line_class[] add_enrich;
Entry_type_enum entryType;
int timepoint;
string sample_name;
for (int indexCol = 0; indexCol < col_length; indexCol++)
{
entryType = data.ColChar.Columns[indexCol].EntryType;
timepoint = data.ColChar.Columns[indexCol].Timepoint;
sample_name = (string)data.ColChar.Columns[indexCol].SampleName.Clone();
symbols = data.Get_alphabetically_ordered_ncbi_official_symbols__with_non_empty_entries_in_indicated_column(indexCol);
add_enrich = Generate_enrichment_lines_and_calculate_pvalues(symbols, entryType, timepoint, sample_name);
add_enrich = Add_missing_process_information(add_enrich);
add_enrich = Add_upregulated_downregulated_symbol_information(add_enrich, data, indexCol);
enrich_list.AddRange(add_enrich);
}
Ontology_enrichment_line_class[] enrich_array = Add_missing_process_information(enrich_list.ToArray());
Ontology_enrichment_class enrich = new Ontology_enrichment_class();
enrich.Add_other_lines(enrich_array);
return(enrich);
}
public void Analyze_de_instance(Data_class data, string base_file_name)
{
this.Base_file_name = (string)base_file_name.Clone();
Data_class data_sep = Generate_data_instance_with_separated_or_combined_entries(data);
data_sep.Set_all_ncbi_official_gene_symbols_to_upper_case();
Ontology_enrichment_class standard_onto_enrich_standard;
Ontology_enrichment_class standard_onto_enrich_filtered = Do_standard_enrichment_analysis_and_write_results(data_sep, out standard_onto_enrich_standard);
Ontology_enrichment_class dynamic_onto_enrich_filtered = Do_dynamic_enrichment_analysis_for_mbco_and_write(standard_onto_enrich_standard, data_sep);
Write_parent_child_network_for_results_of_standard_enrichment_analysis(standard_onto_enrich_filtered);
Write_scp_network_for_results_of_dynamic_enrichment_analsyis(dynamic_onto_enrich_filtered, standard_onto_enrich_filtered);
Write_legend_for_networks(base_file_name);
}
private Data_class Generate_data_instance_with_separated_or_combined_entries(Data_class data)
{
if (Options.Report)
{
Report_class.WriteLine("{0}: Prepare data for enrichment analysis", typeof(Mbc_enrichment_pipeline_class).Name);
}
bool positive_entries_exist = false;
bool negative_entries_exist = false;
int data_length = data.Data_length;
Data_line_class data_line;
int col_length = data.ColChar.Columns_length;
for (int indexData = 0; indexData < data_length; indexData++)
{
data_line = data.Data[indexData];
for (int indexCol = 0; indexCol < col_length; indexCol++)
{
if (data_line.Columns[indexCol] > 0)
{
positive_entries_exist = true;
}
else if (data_line.Columns[indexCol] < 0)
{
negative_entries_exist = true;
}
}
}
if ((positive_entries_exist) && (negative_entries_exist))
{
Data_class data_sep = new Data_class();
if (Options.Data_value_signs_of_interest.Contains(Data_value_signs_of_interest_enum.Combined))
{
data_sep.Add_other_data_instance(data);
}
if (Options.Data_value_signs_of_interest.Contains(Data_value_signs_of_interest_enum.Upregulated))
{
data_sep.Add_other_data_instance(data.Get_data_instance_with_only_upregulated_entries());
}
if (Options.Data_value_signs_of_interest.Contains(Data_value_signs_of_interest_enum.Downregulated))
{
data_sep.Add_other_data_instance(data.Get_data_instance_with_only_downregulated_entries());
}
return(data_sep);
}
else
{
return(data);
}
}
private Ontology_enrichment_line_class[] Add_upregulated_downregulated_symbol_information(Ontology_enrichment_line_class[] enrichment_lines, Data_class data, int indexCol)
{
int de_symbols_length = data.Data_length;
Data_line_class data_line;
Dictionary <string, float> symbol_value_dict = new Dictionary <string, float>();
for (int indexS = 0; indexS < de_symbols_length; indexS++)
{
data_line = data.Data[indexS];
if (data_line.Columns[indexCol] != 0)
{
symbol_value_dict.Add(data_line.NCBI_official_symbol, data_line.Columns[indexCol]);
}
}
enrichment_lines = enrichment_lines.OrderBy(l => l.Scp_name).ToArray();
int enrich_length = enrichment_lines.Length;
Ontology_enrichment_line_class enrich_line;
string symbol;
int overlap_symbols_length;
for (int indexE = 0; indexE < enrich_length; indexE++)
{
enrich_line = enrichment_lines[indexE];
overlap_symbols_length = enrich_line.Overlap_symbols.Length;
for (int indexS = 0; indexS < overlap_symbols_length; indexS++)
{
symbol = (string)enrich_line.Overlap_symbols[indexS].Clone();
enrich_line.Overlap_symbols[indexS] = symbol + " (" + symbol_value_dict[symbol] + ")";
}
}
return(enrichment_lines);
}
private Ontology_enrichment_class Do_dynamic_enrichment_analysis_for_mbco_and_write(Ontology_enrichment_class mbco_onto_enrich_standard, Data_class data)
{
if (Options.Report)
{
Report_class.WriteLine("{0}: Do dynamic enrichment analysis and write results", typeof(Mbc_enrichment_pipeline_class).Name);
}
string subdirectory = Get_results_subdirectory_for_indicated_ontology(Ontology_type_enum.Molecular_biology_cell);
mbco_onto_enrich_standard.Order_by_complete_sample_pvalue();
int mbco_onto_enrich_length = mbco_onto_enrich_standard.Enrich.Length;
Ontology_enrichment_line_class enrich_line;
MBCO_association_line_class[] new_mbco_association_lines;
MBCO_association_class new_mbco_association;
List <Ontology_enrichment_line_class> current_onto_enrich = new List <Ontology_enrichment_line_class>();
Ontology_fisher_class mbco_fisher_dynamic;
int col_length = data.ColChar.Columns.Length;
Data_class current_data;
Colchar_column_line_class current_column_line;
Ontology_enrichment_class current_dynamic_onto_enrich;
Ontology_enrichment_class complete_dynamic_onto_enrich = new Ontology_enrichment_class();
List <Ontology_enrichment_line_class> dynamic_onto_enrich_list = new List <Ontology_enrichment_line_class>();
int added_standard_results_count = 0;
for (int indexCol = 0; indexCol < col_length; indexCol++)
{
current_data = data.Deep_copy();
current_data.Keep_only_input_columns_and_remove_all_rows_that_are_left_over_with_only_zero_values(indexCol);
current_column_line = current_data.ColChar.Columns[0];
current_onto_enrich.Clear();
for (int indexMbco = 0; indexMbco < mbco_onto_enrich_length; indexMbco++)
{
enrich_line = mbco_onto_enrich_standard.Enrich[indexMbco];
if ((enrich_line.EntryType.Equals(current_column_line.EntryType)) &&
(enrich_line.Timepoint.Equals(current_column_line.Timepoint)) &&
(enrich_line.Sample_name.Equals(current_column_line.SampleName)))
{
current_onto_enrich.Add(enrich_line);
added_standard_results_count++;
}
}
if (current_onto_enrich.Count == 0)
{
throw new Exception();
}
new_mbco_association_lines = Generate_new_mbco_association_lines_by_merging_neighboring_scps(current_onto_enrich.ToArray());
new_mbco_association = new MBCO_association_class();
new_mbco_association.Add_to_array(new_mbco_association_lines);
mbco_fisher_dynamic = new Ontology_fisher_class();
mbco_fisher_dynamic.Generate(new_mbco_association, Ontology_type_enum.Molecular_biology_cell, this.Final_bg_genes);
current_dynamic_onto_enrich = mbco_fisher_dynamic.Analyse_data_instance(current_data);
complete_dynamic_onto_enrich.Add_other(current_dynamic_onto_enrich);
}
if (added_standard_results_count != mbco_onto_enrich_standard.Enrich.Length)
{
throw new Exception();
}
complete_dynamic_onto_enrich.Add_other(mbco_onto_enrich_standard);
complete_dynamic_onto_enrich.Keep_only_enrichment_lines_of_indicated_levels(Options.Scp_levels_for_dynamicEnrichment);
complete_dynamic_onto_enrich.Write(subdirectory, "Dynamic_enrichment_results.txt");
Ontology_enrichment_class complete_dynamic_onto_enrich_filtered = complete_dynamic_onto_enrich.Deep_copy();
complete_dynamic_onto_enrich_filtered.Keep_enrichment_lines_below_pvalue_cutoff(Options.Maximum_pvalue_for_standardDynamicEnrichment);
complete_dynamic_onto_enrich_filtered.Keep_top_x_predictions_per_level_for_each_sample(Options.Kept_top_predictions_dynamicEnrichment_per_level);
complete_dynamic_onto_enrich_filtered.Keep_top_x_predictedSCPs_as_part_of_SCPunit_or_singleSCPs(Options.Kept_singleSCPs_dynamicEnrichment_per_level);
complete_dynamic_onto_enrich_filtered.Write(subdirectory, "Dynamic_enrichment_results_filtered.txt");
return(complete_dynamic_onto_enrich_filtered);
}
private Ontology_enrichment_class Do_standard_enrichment_analysis_and_write_results(Data_class data, out Ontology_enrichment_class onto_enrich)
{
if (Options.Report)
{
Report_class.WriteLine("{0}: Do standard enrichment analysis and write results", typeof(Mbc_enrichment_pipeline_class).Name);
}
onto_enrich = this.MBCO_fisher_standard.Analyse_data_instance(data);
Ontology_type_enum ontology = Ontology_type_enum.Molecular_biology_cell;
string subdirectory = Get_results_subdirectory_for_indicated_ontology(ontology);
onto_enrich.Write(subdirectory, "Standard_enrichment_results.txt");
Ontology_enrichment_class onto_enrich_filtered = onto_enrich.Deep_copy();
onto_enrich_filtered.Keep_enrichment_lines_below_pvalue_cutoff(Options.Maximum_pvalue_for_standardDynamicEnrichment);
onto_enrich_filtered.Keep_top_x_predictions_per_level_for_each_sample(Options.Kept_top_predictions_standardEnrichment_per_level);
onto_enrich_filtered.Write(subdirectory, "Standard_enrichment_results_filtered.txt");
return(onto_enrich_filtered);
}
