Testing the package

The phuEGO package contains a test dataset, which is a list of differentially phosphorylated proteins (after phosphosite aggregation) between untreated cells and those treated with epidermal growth factor (EGF) (PMID: 19651622). To view the test dataset, run the following Python code:

from phuego import load_test_example

# Path and a dataframe of the test dataset.
test_path, test_df = load_test_example()
print(test_path) #user can use this to access the file.
print(test_df)

Mock run

A mock run performs 10 network propagations on the randomized networks using the test dataset as input, which isn’t sufficient for reliable statistics. But as it typically finishes within a few minutes, it can help understanding the package.

Important note: carefully provide the kde_cutoff(-k) and fisher genesets(-fg) as list of float numbers or strings. Refer to the command help messages for further details.

# Folders won't be automatically created if not existing.
mkdir "path/to/desired_result_folder"

# Performing a mock run with default parameter values.
phuego mock\
 -sf "path/to/support_data_folder/"\
 -rf "path/to/desired_result_folder/"\

# Showcasing the usage of parameters.
phuego mock\
 -sf "path/to/support_data_folder/"\
 -rf "path/to/desired_result_folder/"\
 -ds 0.85\
 -de 0.85\
 -dm 0.85\
 -k "[0.85, 0.9]"\
 -fg "['K', 'B']"\

Warning

For Windows users, please provide the paths with forward slash ‘/’ instead of backward slash ‘\’.

Test run

A test run is similar to the mock run, but performs a complete analysis with 1000 propagation on randomized networks. It takes longer to finish (typically 10-30 min).

# Performing a test run with default parameters.
phuego test\
 -sf "path/to/support_data_folder/"\
 -rf "path/to/desired_result_folder/"\