LEA (version 1.4.0)

Q: Admixture coefficients from a snmf run

Description

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

Usage

Q(object, K, run)

Arguments

object

A snmfProject object.

K

The number of ancestral populations.

run

A chosen run.

Value

res

A matrix containing the admixture coefficients for the chosen run with K ancestral populations.

See Also

geno snmf G cross.entropy

Examples

### Example of analyses using snmf ###

# creation of the genotype file, genotypes.geno.
# It contains 400 SNPs for 50 individuals.
data("tutorial")
write.geno(tutorial.R, "genotypes.geno")

################
# runs of snmf #
################

# main options, K: (the number of ancestral populations), 
#        entropy: calculate the cross-entropy criterion, 
#        CPU: the number of CPUs.

# Runs with K between 1 and 5 with cross-entropy and 2 repetitions.
project = NULL
project = snmf("genotypes.geno", K = 3, repetitions = 2, project = "new")

# get the ancestry coefficients for the 2nd run for K = 3. 
res = Q(project, K = 3, run = 2)

# plot the 2nd run for K = 3 (ancestry coefficients).
barplot(t(Q(project, K = 3, run = 2)))