Run ADMIXTURE from R — gt_admixture • tidypopgen

This function runs ADMIXTURE, taking either a gen_tibble or a file as an input. This is a wrapper that runs ADMIXTURE from the command line, and reads the output into R. It can run multiple values of k and multiple repeats for each k.

Usage

gt_admixture(
  x,
  k,
  n_runs = 1,
  crossval = FALSE,
  n_cores = 1,
  seed = NULL,
  conda_env = "none"
)

Arguments

x: a gen_tibble or a character giving the path of the input PLINK bed file
k: an integer giving the number of clusters
n_runs: the number of runs for each k value (defaults to 1)
crossval: boolean, should cross validation be used to assess the fit (defaults ot FALSE)
n_cores: number of cores (defaults to 1)
seed: the seed for the random number generator (defaults to NULL)
conda_env: the name of the conda environment to use. "none" forces the use of a local copy, whilst any other string will direct the function to use a custom conda environment.

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 cross validation error (if crossval 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 command line program ADMIXTURE. It can either use a binary present in the main environment, or use a copy installed in a conda environment.