Run SNMF from R in tidypopgen

Usage

gt_snmf(
  x,
  k,
  project = "continue",
  n_runs = 1,
  alpha,
  tolerance = 1e-05,
  entropy = FALSE,
  percentage = 0.05,
  I,
  iterations = 200,
  ploidy = 2,
  seed = -1
)

Arguments

x: a gen_tibble or a character giving the path to the input geno file
k: an integer giving the number of clusters
project: one of "continue", "new", and "force": "continue" stores files in the current project, "new" creates a new project, and "force" stores results in the current project even if the .geno input file has been altered,
n_runs: the number of runs for each k value (defaults to 1)
alpha: numeric snmf regularization parameter. See LEA::snmf for details
tolerance: numeric value of tolerance (default 0.00001)
entropy: boolean indicating whether to estimate cross-entropy
percentage: numeric value indicating percentage of masked genotypes, ranging between 0 and 1, to be used when entropy = TRUE
I: number of SNPs for initialising the snmf algorithm
iterations: numeric integer for maximum iterations (default 200)
ploidy: the ploidy of the input data (defaults to 2)
seed: the seed for the random number generator

Value

an object of class gt_admix consisting of a list with the following elements:

k the number of clusters
Q a matrix with the admixture proportions
P a matrix with the allele frequencies
log a log of the output generated by ADMIXTURE (usually printed on the screen when running from the command line)
cv the masked cross-entropy (if entropy is TRUE)
loglik the log likelihood of the model
id the id column of the input gen_tibble (if applicable)
group the group column of the input gen_tibble (if applicable)

Details

This is a wrapper for the function snmf from R package LEA.