public void Add_new_mbco_association_lines_after_filtering_for_bg_genes(MBCO_association_class new_mbco_association)
{
if (this.Bg_genes.Length > 0)
{
new_mbco_association.Keep_only_bg_symbols(this.Bg_genes);
}
this.MBCO_association.Add_array_of_other_MBCO_association(new_mbco_association);
}
public void Generate(MBCO_association_class mbco_association, Ontology_type_enum ontology, params string[] bg_symbols)
{
this.Ontology = ontology;
this.Bg_genes = Array_class.Deep_copy_string_array(bg_symbols);
this.MBCO_association = mbco_association.Deep_copy();
if (this.Bg_genes.Length > 0)
{
MBCO_association.Keep_only_bg_symbols(bg_symbols);
}
}
private void Generate_mbco_association(string[] bg_genes)
{
if (Options.Report)
{
Report_class.WriteLine("{0}: Generate MBCO gene-SCP association networks", typeof(Mbc_enrichment_pipeline_class).Name);
}
MBCO_association = new MBCO_association_class();
MBCO_association.Generate_by_reading_safed_file();
string[] all_mbco_genes = MBCO_association.Get_all_distinct_ordered_symbols();
if (bg_genes.Length > 0)
{
this.Exp_bg_genes = Array_class.Deep_copy_string_array(bg_genes);
this.Final_bg_genes = Overlap_class.Get_intersection(this.Exp_bg_genes, all_mbco_genes);
}
else
{
this.Exp_bg_genes = new string[0];
this.Final_bg_genes = Array_class.Deep_copy_string_array(all_mbco_genes);
}
this.MBCO_association.Keep_only_bg_symbols(this.Final_bg_genes);
this.MBCO_association.Remove_background_genes_scp();
this.MBCO_fisher_standard = new Ontology_fisher_class();
this.MBCO_fisher_standard.Generate(this.MBCO_association, Ontology_type_enum.Molecular_biology_cell, this.Final_bg_genes);
}
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);
}
