py-coloc

A pure-Python port of the R/CRAN package coloc — Bayesian colocalisation of two genetic traits.

pycoloc tests whether two genetic traits (for example a GWAS trait and a molecular QTL) share one or more causal variants in a genomic region, using Approximate Bayes Factors. It is a faithful re-implementation of coloc 5.2.3 — the posterior probabilities match the R package to machine precision (< 1e-4 absolute, typically < 1e-15).

• Methods: Giambartolomei et al., PLoS Genet. 2014 (single causal variant); Wallace, PLoS Genet. 2020 / 2021 (SuSiE & conditioning); Wakefield, Genet. Epidemiol. 2009 (Approximate Bayes Factors).
• Dependencies: numpy, scipy, pandas, matplotlib only. No R, no rpy2.

Installation

pip install pycoloc

The five posterior hypotheses

coloc_abf returns five posterior probabilities for a region:

Quick start

A dataset is a plain dict of GWAS summary statistics for one trait.

import numpy as np
import pycoloc as cl

# two traits, each with one (shared) causal SNP
rng = np.random.default_rng(0)
n = 500
def make(causal):
    beta = rng.normal(0, 0.02, n)
    beta[causal] = 0.4
    return dict(
        snp=[f"s{i}" for i in range(n)],
        position=np.arange(n) * 1000,
        beta=beta, varbeta=np.full(n, 0.0025),
        MAF=rng.uniform(0.05, 0.5, n),
        type="quant", N=4000, sdY=1.0,
    )

D1, D2 = make(250), make(250)
res = cl.coloc_abf(D1, D2)
print(res["summary"])          # nsnps, PP.H0.abf ... PP.H4.abf
print(res["results"].head())   # per-SNP lABF and SNP.PP.H4

Single-causal-variant colocalisation

res  = cl.coloc_abf(D1, D2, p1=1e-4, p2=1e-4, p12=1e-5)
fm   = cl.finemap_abf(D1)          # single-trait ABF fine-mapping
det  = cl.coloc_detail(D1, D2)     # also returns the all-pairs H3 grid

Multiple causal variants (SuSiE)

coloc_susie consumes the per-single-effect log-Bayes-factor matrix lbf_variable (shape L x p) produced by susieR::runsusie — it does not run SuSiE itself, so there is no SuSiE dependency.

# lbf1, lbf2 : (L x p) arrays from runsusie(); cs_index : credible sets
res = cl.coloc_susie(lbf1, lbf2,
                     snps1=snp_names, snps2=snp_names,
                     cs_index1=[1], cs_index2=[1])
print(res["summary"])   # one row per credible-set pair, PP.H0..H4

You may also pass susie-like dicts carrying lbf_variable and sets.

Multiple-signal colocalisation by conditioning / masking

# requires beta, varbeta, MAF, N and an LD matrix in each dataset
res = cl.coloc_signals(D1, D2, method="cond", p12=1e-5)  # conditioning
res = cl.coloc_signals(D1, D2, method="mask", p12=1e-5)  # masking

Prior-sensitivity analysis

res  = cl.coloc_abf(D1, D2)
sens = cl.sensitivity(res, "H4 > 0.5", dataset1=D1, dataset2=D2)

sensitivity sweeps the p12 prior, reports the range over which the rule holds, and (with doplot=True) draws the four-panel coloc sensitivity figure.

Plots

cl.plot_coloc_abf(res)   # per-SNP |z| coloured by SNP.PP.H4, per trait
cl.plot_dataset(D1)      # Manhattan plot of one dataset
cl.manhattan(res)        # per-SNP posterior Manhattan

Public API

coloc_abf, coloc_detail, finemap_abf, combine_abf, ColocABF, coloc_susie, coloc_bf_bf, finemap_susie, finemap_bf, logbf_to_pp, coloc_signals, finemap_signals, coloc_process, est_cond, est_all_cond, find_best_signal, map_cond, map_mask, bin2lin, sensitivity, plot_coloc_abf, plot_dataset, manhattan, process_dataset, check_dataset, check_alignment, check_ld, subset_dataset, approx_bf_estimates, approx_bf_p, sdY_est, logsum, logdiff, Var_data, Var_data_cc, adjust_prior, prior_snp2hyp, prior_adjust.

R parity

tests/r_reference_driver.R runs coloc 5.2.3 on the bundled coloc_test_data and exports both the raw inputs and the reference results; tests/test_r_parity.py then runs pycoloc on the identical inputs. On coloc_test_data (500 SNPs):

python -m pytest tests/ -q

License

GPL-3, matching the upstream coloc package (License: GPL in its DESCRIPTION).

Citing

If you use pycoloc, please cite the original coloc methods papers:

• Giambartolomei C et al. (2014) Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet. 10(5):e1004383.
• Wallace C (2020) Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses. PLoS Genet. 16(4):e1008720.
• Wallace C (2021) A more accurate method for colocalisation analysis allowing for multiple causal variants. PLoS Genet. 17(9):e1009440.