public Leave_out_scp_scp_network_options_class Deep_copy()
{
Leave_out_scp_scp_network_options_class copy = (Leave_out_scp_scp_network_options_class)this.MemberwiseClone();
copy.Top_quantile_of_considered_SCP_interactions_per_level = Array_class.Deep_copy_array(this.Top_quantile_of_considered_SCP_interactions_per_level);
return(copy);
}
public Ontology_fisher_class Deep_copy()
{
Ontology_fisher_class copy = (Ontology_fisher_class)this.MemberwiseClone();
copy.MBCO_association = this.MBCO_association.Deep_copy();
copy.Bg_genes = Array_class.Deep_copy_string_array(this.Bg_genes);
return(copy);
}
public Mbc_add_inferred_parentSCP_line_class Deep_copy()
{
Mbc_add_inferred_parentSCP_line_class copy = (Mbc_add_inferred_parentSCP_line_class)this.MemberwiseClone();
copy.Inferred_parentSCP = (string)this.Inferred_parentSCP.Clone();
copy.Children_scps = Array_class.Deep_copy_string_array(this.Children_scps);
return(copy);
}
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);
}
}
public void Add_ancestors_of_missing_levels(MBCO_obo_network_class mbco_obo_network_parent_child)
{
MBCO_obo_network_class mbco_obo_network_child_parent = mbco_obo_network_parent_child.Deep_copy_mbco_obo_nw();
mbco_obo_network_child_parent.Transform_into_child_parent_direction();
MBCO_obo_network_class current_mbco_obo_network;
int[] levels_in_scp = this.Scp_nw.Nodes.Get_all_levels();
int levels_in_scp_length = levels_in_scp.Length;
int level_in_scp;
int max_level_in_scp = -1;
for (int indexLevelScp = 0; indexLevelScp < levels_in_scp_length; indexLevelScp++)
{
level_in_scp = levels_in_scp[indexLevelScp];
if ((max_level_in_scp == -1) ||
(max_level_in_scp < level_in_scp))
{
max_level_in_scp = level_in_scp;
}
}
int[] levels_in_mbco = mbco_obo_network_child_parent.Nodes.Get_all_levels();
int[] add_levels_preliminary = Overlap_class.Get_part_of_list1_but_not_of_list2(levels_in_mbco, levels_in_scp);
List <int> add_levels_list = new List <int>();
foreach (int add_level_preliminary in add_levels_preliminary)
{
if ((add_level_preliminary < max_level_in_scp) && (add_level_preliminary != 0))
{
add_levels_list.Add(add_level_preliminary);
}
}
int[] add_levels = add_levels_list.ToArray();
add_levels = add_levels.OrderByDescending(l => l).ToArray();
int add_length = add_levels.Length;
int add_level;
string[] add_parents;
string[] children;
string[] keep_nodes;
for (int indexAdd = 0; indexAdd < add_length; indexAdd++)
{
add_level = add_levels[indexAdd];
level_in_scp = add_level + 1;
children = this.Scp_nw.Nodes.Get_all_nodeNames_of_indicated_levels(level_in_scp);
add_parents = mbco_obo_network_child_parent.Get_all_parents_if_direction_is_child_parent(children);
current_mbco_obo_network = mbco_obo_network_parent_child.Deep_copy_mbco_obo_nw();
keep_nodes = Array_class.Get_ordered_union(add_parents, children);
current_mbco_obo_network.Keep_only_input_nodeNames(keep_nodes);
this.Scp_nw.Merge_this_network_with_other_network(current_mbco_obo_network);
}
}
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);
}
