em_li: EM algorithm from Li (2011)

In segtest: Tests for Segregation Distortion in Polyploids

EM algorithm from Li (2011)

Description

EM algorithm to estimate prior genotype probabilities from genotype likelihoods.

Usage

em_li(B, itermax = 100L, eps = 1e-05)

Arguments

B	Matrix of genotype log-likelihoods. The rows index the individuals and the columns index the genotypes.
itermax	The maximum number of iterations.
eps	The stopping criteria.

Value

A vector of log prior probabilities for each genotype.

Author(s)

David Gerard

References

• Li, H. (2011). A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics, 27(21), 2987-2993. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btr509")}

Examples

# Simulate some data
set.seed(1)
gl <- simgl(nvec = c(3, 2, 4, 1, 2))
# Run em
lprob <- em_li(B = gl)
# Exponentiate to get probabilities
prob <- exp(c(lprob))
prob

segtest documentation built on July 1, 2025, 1:07 a.m.