G {LEA}R Documentation

Ancestral allele frequencies from a snmf run

Description

Return the snmf output matrix of ancestral allele frequency matrix for the chosen run with K ancestral populations. For an example, see snmf.

Usage

G(object, K, run)

Arguments

object

A snmfProject object.

K

The number of ancestral populations.

run

A chosen run.

Value

res

A matrix containing the ancestral allele frequencies for a run with K ancestral populations.

Author(s)

Eric Frichot

See Also

geno snmf Q cross.entropy

Examples

### Example of analyses using snmf ###

# creation of a genotype file: genotypes.geno.
# The data contain 400 SNPs for 50 individuals.
data("tutorial")
write.geno(tutorial.R, "genotypes.geno")

################
# running snmf #
################


# Two runs for K = 1 to 5 
project.snmf = snmf("genotypes.geno", 
                K = 3, 
                repetitions = 2, 
                project = "new")

# get the ancestral genotype frequency matrix, G, for the 2nd run for K = 3. 
freq = G(project.snmf, K = 3, run = 2)

[Package LEA version 2.2.0 Index]