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]
-
-n
,
--network
<network>
¶ Path to the network graph or kernel [required]
-
-o
,
--output
<output>
¶ Output file
-
-m
,
--method
<method>
¶ Diffusion method
- Options
mc|ber_s|ber_p|gm|raw|ml|z
-
-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).
-
-t
,
--threshold
<threshold>
¶ Codify node labels by applying a threshold to logFC in input.
-
-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.
-
-p
,
--p_value
<p_value>
¶ Statistical significance (p-value). [default: 0.05]
-
-f
,
--output_format
<output_format>
¶ Statistical significance (p-value). [default: csv]