em: Do ancestry analysis with EM algorithm

In radmixture: Calculate Population Stratification

Description

The EM algorithm could be used for estimating the Q and F matrix.

Usage

em(g, q, f, acc, max.iter, tol, model)

Arguments

g	Genotype matrix with dimensions n × p, where n is sample size and p is the number of SNPs.
q	Ancestry coefficient matrix with dimensions n × K, where n is sample size and K is the number of populations.
f	Minor allele frequency matrix with dimensions K × p, where K is the number of populations and p is the number of SNPs.
acc	a logical value indicating whether use accelerated EM or not.
max.iter	an integer. If acc is TRUE, the number of iterations must be set. max.iter should greater than 1.
tol	Tolerance. If acc is FALSE, tol must be set. The default is 1e-4.
model	Choose which model you want to use. Supervised learning or unsupervised learning.

Value

Estimation results of q, f and the loglikelihood value of each iteration.

radmixture documentation built on May 2, 2019, 6:11 a.m.