Run ADMIXTURE Cross-Validation

Runs external ADMIXTURE analyses and parses cross-validation errors.

Usage

run_admixture_cv(executable, plink_prefix, k_values, threads = 1L,
  cv_folds = 5L, output_dir = ".", seed = 42L, timeout_seconds = 14400)

Arguments

executable

Path or command name for the ADMIXTURE executable.

plink_prefix

Prefix of a PLINK BED/BIM/FAM dataset.

k_values

Integer vector of K values.

threads

Number of ADMIXTURE threads.

cv_folds

Number of cross-validation folds.

output_dir

Directory for logs and Q/P files.

seed

Random seed exposed to ADMIXTURE through the environment.

timeout_seconds

Maximum wall-clock seconds allowed per K value before ADMIXTURE (and its full process tree) is killed and treated as a failure.

Value

A data table containing cross-validation error by K.