Man pages for DrDimont
Drug Response Prediction from Differential Multi-Omics Networks
| calculate_interaction_score | [INTERNAL] Calls a python script to calculate interaction... |
| check_connection | [INTERNAL] Check connection |
| check_drug_target | [INTERNAL] Check drug target interaction data |
| check_drug_targets_in_layers | [INTERNAL] Check drug target and layer data |
| check_input | Check pipeline input data for required format |
| check_layer | [INTERNAL] Check layer input |
| check_sensible_connections | [INTERNAL] Check connection and layer data |
| chunk | [INTERNAL] Create chunks from a vector for parallel computing |
| chunk_2gether | [INTERNAL] Create chunks from two vectors for parallel... |
| combined_graphs_example | Combined graphs |
| combine_graphs | [INTERNAL] Combine graphs by adding inter-layer edges |
| compute_correlation_matrices | Computes correlation matrices for specified network layers |
| compute_drug_response_scores | Calculate drug response score |
| corPvalueStudentParallel | [INTERNAL] Compute p-values for upper triangle of correlation... |
| correlation_matrices_example | Correlation matrices |
| create_unique_layer_node_ids | [INTERNAL] Assign node IDs to the biological identifiers... |
| determine_drug_targets | Determine drug target nodes in network |
| differential_graph_example | Differential graph |
| drdimont_settings | Create global settings variable for DrDimont pipeline |
| drug_gene_interactions | Drug-gene interactions |
| drug_response_scores_example | Drug response score |
| drug_target_edges_example | Drug target nodes in combined network |
| find_targets | [INTERNAL] Filter drug target nodes |
| generate_combined_graphs | Combines individual layers to a single graph |
| generate_differential_score_graph | Compute difference of interaction score of two groups |
| generate_individual_graphs | Builds graphs from specified network layers |
| generate_interaction_score_graphs | Computes interaction score for combined graphs |
| generate_reduced_graph | [INERNAL] Generate a reduced iGraph from adjacency matrices |
| get_layer | [INTERNAL] Fetch layer by name from layer object |
| get_layer_setting | [INTERNAL] Get layer (and group) settings |
| graph_metrics | [INTERNAL] Analysis of metrics of an iGraph object |
| individual_graphs_example | Individual graphs |
| install_python_dependencies | Installs python dependencies needed for interaction score... |
| interaction_score_graphs_example | Interaction score graphs |
| inter_layer_edgelist_by_id | [INTERNAL] Inter layer connections by identifiers |
| inter_layer_edgelist_by_table | [INTERNAL] Interaction table to iGraph graph object |
| layers_example | Formatted layers object |
| load_interaction_score_output | [INTERNAL] Loads output of python script for interaction... |
| make_connection | Specify connection between two individual layers |
| make_drug_target | Reformat drug-target-interaction data |
| make_layer | Creates individual molecular layers from raw data and unique... |
| metabolite_data | Metabolomics data |
| metabolite_protein_interactions | Metabolite protein interaction data |
| mrna_data | mRNA expression data |
| network_reduction_by_pickHardThreshold | [INTERNAL] Reduces network based on WGCNA::pickHardThreshold... |
| network_reduction_by_p_value | [INTERNAL] Reduce the the entries in an adjacency matrix by... |
| phosphosite_data | Phosphosite data |
| pipe | Pipe operator |
| protein_data | Protein data |
| return_errors | Return detected errors in the input data |
| run_pipeline | Execute all DrDimont pipeline steps sequentially |
| sample_size | [INTERNAL] Sample size for correlation computation |
| set_cluster | [INTERNAL] Create and register cluster |
| shutdown_cluster | [INTERNAL] Shutdown cluster and remove corresponding... |
| target_edge_list | [INTERNAL] Get edges adjacent to target nodes |
| write_interaction_score_input | [INTERNAL] Write edge lists and combined graphs to files |
