gt_snmf: Run SNMF from R in tidypopgen

In tidypopgen: Tidy Population Genetics

Run SNMF from R in tidypopgen

Description

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

Details

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

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)

Examples

# run the example only if we have the package installed
example_gt <- load_example_gt("gen_tbl")

# To run SNMF on a gen_tibble:
example_gt %>% gt_snmf(
  k = 1:3, project = "force", entropy = TRUE,
  percentage = 0.5, n_runs = 1, seed = 1, alpha = 100
)

tidypopgen documentation built on Aug. 28, 2025, 1:08 a.m.