nta

Run single-omic NTA (Network-topology based analysis) with files at the provided paths

Parameters

• edge_list_path - String of the path to the edge list file of the network. See below for details.
• analyte_list_path - String of the path to the rank file of interest, with analytes separated by new lines
• nta_method - a NTAMethod object specifying the NTA method for the analysis.
• n - the number of seeds or nodes to identify according to nta_method

Returns

Returns a dictionary object containing the candidates (seed nodes when using prioritization), scores (random-walk probabilities), and neighborhood (identified nodes)

Panics

Panics if the network or the analyte file is malformed or not at specified path. Will also panic if nta_method is not specified correctly

Example

import webgestaltpy

nta_method = webgestaltpy.NTAMethod.Prioritization
y = webgestaltpy.nta("data/hsapiens_network_CPTAC_Proteomics_OV_entrezgene.net", "data/net_genes.txt", nta_method, 5)
print(y)

Output

{
  'candidates': [
    'ACTA1',
    'ACTA2',
    'ACTB',
    'ACTG1'
  ],
  'scores': [
    0.015611545101449542,
    0.015611545101449542,
    0.015227515228472441,
    0.015227515228472441,
    0.015105514420304793
  ],
  'neighborhood': [
    'ACTA1',
    'ACTA2',
    'ACTB',
    'ACTG1',
    'ACTG2'
  ]
}