PDGrapher/data/scripts/GRN/README.md

Scripts to build GRN for PDGrapher

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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)
• 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