| ## Scripts to build GRN for PDGrapher | |
| --- | |
| ### 1. Generate Expression Matrices | |
| Use `xpr_matrix_generator_datatypesplit.py` to build the `xpr_matrices` files. | |
| **Inputs:** | |
| - `level3_beta_ctl_n188708x12328.gctx` (download from [C-map](https://clue.io/releases/data-dashboard)) | |
| - `ppi_all_genes_edgelist.txt` (see `data/scripts/ppi` for instructions on generating this file) | |
| **Command Example:** | |
| python xpr_matrix_generator_datatypesplit.py | |
| ### 2. Generate GENIE3 edge list | |
| Use `GENIEppi-run.py` to build the `{cell_line}_{pert_type}_edgelist.txt` files. | |
| **Inputs:** | |
| - `xpr_matrices` (from step 1) | |
| **Command Example:** | |
| python GENIEppi-run.py --data_type cmp --cell_line A549 | |
| ### 3. Filter edge lists | |
| Use `filter_edge_list.py` to build the `{cell_line}_{pert_type}_edgelist_filtered.txt` files. | |
| **Inputs:** | |
| - `{cell_line}_{pert_type}_edgelist.txt` files (from step 2) | |
| **Command Example:** | |
| python filter_edge_list.py --data_type cmp --cell_line A549 | |