geno1: Calculates P(G|H)

In thoree/inbred: Different functions related to LR, bootstrap etc

Description

The marker data for one individual at two markers is G = (a1/a2, b1/b2). H is a n by n matrix of haplotype probabilities

Usage

geno1(a1, a2, b1, b2, H)

Arguments

a1	First allele, first marker
a2	Second allele, first marker
b1	First allele, second marker
b2	Second allele, second marker

Value

P(G|H)

Examples

# Below I go through some cases trying to figure out
# what the LD probabilities should be

p = q = c(0.1, 0.2, 0.3, 0.4)
# Checks when LE
H = p%o%q # Haplotype probs for LE

abs(geno1(1, 1, 1, 1, H) - p[1]^2*q[1]^2) < 1e-15
abs(geno1(1, 2, 3, 3, H) - 2*p[1]*p[2]*q[3]^2) < 1e-15
abs(geno1(1, 2, 3, 4, H) - 2*p[1]*p[2]*2*q[3]*q[4]) < 1e-15
abs(geno1(2, 2, 4, 4, H) - p[2]^2*q[4]^2) < 1e-15

thoree/inbred documentation built on March 28, 2021, 7:42 p.m.