DIALECT

Driver Interactions and Latent Exclusivity or Co-occurrence in Tumors

DIALECT identifies mutually exclusive (ME) and co-occurring (CO) driver mutation pairs by modeling each somatic count as passenger background + latent driver, conditioned on a background mutation rate (BMR).

pip install -e ".[dev]"
dialect generate -m cohort.maf -o out/cohort
dialect identify -c out/cohort/count_matrix.csv -b out/cohort/bmr_pmfs.csv -o out/cohort -k 100

from dialect import estimate_bmr, identify_interactions
estimate_bmr("cohort.maf", "out/cohort", provider="cbase")
result = identify_interactions(
    "out/cohort/count_matrix.csv", "out/cohort/bmr_pmfs.csv", "out/cohort", top_k=100
)

Agent / contributor context: see AGENTS.md.

Cite

@article{shuaibi2024dialect,
  author  = {Ahmed Shuaibi and Uthsav Chitra and Benjamin J. Raphael},
  title   = {A latent variable model for evaluating mutual exclusivity and
             co-occurrence between driver mutations in cancer},
  journal = {bioRxiv},
  year    = {2024},
  doi     = {10.1101/2024.04.24.590995}
}

BSD-3-Clause — see LICENSE.