| Q {LEA} | R Documentation |
Return the snmf output matrix of admixture coefficients for the chosen
run with K ancestral populations. For an example, see snmf.
Q(object, K, run)
object |
A snmfProject object. |
K |
The number of ancestral populations. |
run |
A chosen run. |
res |
A matrix containing the admixture coefficients for the chosen run with K ancestral populations. |
Eric Frichot
### Example of analysis using snmf ###
# Creation of the genotype file: genotypes.geno.
# The data contain 400 SNPs for 50 individuals.
data("tutorial")
write.geno(tutorial.R, "genotypes.geno")
################
# running snmf #
################
project.snmf <- snmf("genotypes.geno",
K = 3,
repetitions = 2,
project = "new")
# get the ancestry coefficients for the 2nd run for K = 3.
Q.3 <- Q( project.snmf, K = 3, run = 2)
# cluster assignment for each individual
cluster <- apply( Q.3, 1, which.max)
table(cluster)