ora

Run a single-omic ORA with gmt file and list of analytes and reference provided as list of strings.

Parameters

• gmt_path - str of the path to the gmt file of interest
• analyte_list - list[str] of the analyte list of interest.
• reference_list - list[str] of the reference list. Typically all observed analytes.

Returns

Returns a list of dictionaries with the results containing the ORA results for every set.

Panics

Panics if the any file or list is malformed or not at specified path.

Example

import webgestaltpy

def file_to_list(file_path: str) -> list[str]:
    """Convert file to list[str]"""
    with open(file_path, "r") as r:
        return list(r.readlines()

gene_list = file_to_list("genelist.txt")
reference = file_to_list("reference.txt")

res = webgestaltpy.ora("kegg.gmt", gene_list, reference) ## gene_list and reference are both list[str]

print(res[0:2]) ## print first two results

Output

[
  {
    'set': 'has00010',
    'p': 0.7560574551180973,
    'fdr': 1,
    'overlap': 2,
    'expected': 2.6840874707743088,
    'enrichment_ratio': 0.7451321992211519
  },
  {
    'set': 'has00020',
    'p': 0.7019892669020903,
    'fdr': 0.9981116297866582,
    'overlap': 1,
    'expected': 1.1841562371063128,
    'enrichment_ratio': 0.8444831591173054
  }
]