hardy_weinberg.js

const assert = require('assert');

// This is an implementation of the Hardy-Weinberg frequencies in Javascript.
//
// We are going to consider a simple gene with 2 alleles, and 3 genotypes (A1A1, A1A2, A2A2)
// We are going to model this by using p for the frequency of the A1 allele, q for
// the frequency of the A2 allele, and using the HW principle, we get the following frequencies
// based on our original input:
//
//   A1A1 = p * p = p^2
//   A1A2 = p * q = pq
//   A2A1 = q * p = qp  (--> follows from above = 2pq)
//   A2A2 = q * q = q^2
//
// So we get a final polynomial function of p^2 + 2pq + q^2 = 1.

var a1a1 = 0.15;
var a2a2 = 0.35;
var a1a2 = 1 - (a1a1 + a2a2);

var p = a1a1 + (a1a2 / 2);  // Because half of them are from the heterozygous cell
var q = 1 - p;              // Because both of them must add up to 1.

function create_next_generations(runs, first_gen_prob) {
    console.log("generation 0:\t" + a1a1 + "\t" + a1a2 + "\t" + a2a2);

    function _round_number(value, decimals) {
        var shifter = Math.pow(10, decimals);
        return Math.round(value * shifter) / shifter;
    }

    function _next_gen(runs, current_gen, gen_prob) {
        p = gen_prob[0];
        q = gen_prob[1];

        // Now, let's calculate the next generation
        a1a1 = _round_number(p * p, 2);
        a1a2 = _round_number(2 * p * q, 2);
        a2a2 = _round_number(q * q, 2);

        // Verify correctness of the result.
        all = a1a1 + a1a2 + a2a2;
        assert.equal(all, 1);

        next_gen = current_gen+1;

        console.log("generation " + next_gen +":\t" + a1a1 + "\t" + a1a2 + "\t" + a2a2);

        next_generation_probabilities = [a1a1, a1a2, a2a2];
        allelic_probabilities = [p, q];

        if (current_gen == runs-1) {
            return next_generation_probabilities;
        } else {
            _next_gen(runs, current_gen+1, allelic_probabilities);
        }
    }

    return _next_gen(runs, 0, first_gen_prob);
}

create_next_generations(12, [p, q]);