Closed lila167 closed 3 years ago
Hi, @PayamDiba I am trying to use your tool to simulate a simple GRN with 3 genes and 3 cell types. This is how I am using it:
bifurcation_matrix = [[0, 0.8, 0 ],[0, 0, 1.1], [0,0,0]] sim = sergio(number_genes=3, number_bins=3, number_sc=200, noise_params = 0, noise_type = "dpd", decays=0.1, dynamics=True, sampling_state=20, dt=0.01, bifurcation_matrix= bifurcation_matrix)
bifurcation_matrix = [[0, 0.8, 0 ],[0, 0, 1.1], [0,0,0]]
sim = sergio(number_genes=3, number_bins=3, number_sc=200, noise_params = 0, noise_type = "dpd", decays=0.1, dynamics=True, sampling_state=20, dt=0.01, bifurcation_matrix= bifurcation_matrix)
sim.build_graph("input_file_targets.txt", "input_file_regs.txt")
"input_file_targets.txt" is similar to your example:
1, 1, 0, 2.5, 2 2, 1, 1, -1.3, 2
1, 1, 0, 2.5, 2
2, 1, 1, -1.3, 2
and "input_file_regs" is:
0, 0.5, 1.5, 3
However, I get the following error:
Error: Inconsistent number of bins. Would you please help me with that? Thanks
Error: Inconsistent number of bins
I solved the issue :)
lila167
commented
3 years ago lila167
commented
3 years ago
Hi, @PayamDiba I am trying to use your tool to simulate a simple GRN with 3 genes and 3 cell types. This is how I am using it:
bifurcation_matrix = [[0, 0.8, 0 ],[0, 0, 1.1], [0,0,0]]sim = sergio(number_genes=3, number_bins=3, number_sc=200, noise_params = 0, noise_type = "dpd", decays=0.1, dynamics=True, sampling_state=20, dt=0.01, bifurcation_matrix= bifurcation_matrix)sim.build_graph("input_file_targets.txt", "input_file_regs.txt")"input_file_targets.txt" is similar to your example:
1, 1, 0, 2.5, 22, 1, 1, -1.3, 2and "input_file_regs" is:
0, 0.5, 1.5, 3However, I get the following error:
Error: Inconsistent number of bins. Would you please help me with that? Thanks