Command Line Interface¶
DiffuPy Command Line Interface
diffupy¶
DiffuPy
diffupy [OPTIONS] COMMAND [ARGS]...
diffuse¶
Run a diffusion method over a network or pre-generated kernel.
diffupy diffuse [OPTIONS]
Options
-
-i,--input<input>¶ Input data [required]
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-n,--network<network>¶ Path to the network graph or kernel [required]
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-o,--output<output>¶ Output file
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-m,--method<method>¶ Diffusion method
- Options
mc|ber_s|ber_p|gm|raw|ml|z
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-b,--binarize<binarize>¶ If logFC provided in dataset, convert logFC to binary (e.g., up-regulated entities to 1, down-regulated to -1). For scoring methods that accept quantitative values (i.e., raw & z), node labels can also be codified with LogFC (in this case, set binarize==False).
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-t,--threshold<threshold>¶ Codify node labels by applying a threshold to logFC in input.
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-a,--absolute_value<absolute_value>¶ Codify node labels by applying threshold to | logFC | in input. If absolute_value is set to False,node labels will be signed.
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-p,--p_value<p_value>¶ Statistical significance (p-value). [default: 0.05]
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-f,--output_format<output_format>¶ Statistical significance (p-value). [default: csv]