run_admixture: run admixture Reps times at each of K values

Description Usage Arguments

View source: R/plink-admixture-etc.R

Description

Just a wrapper to mclapply over all this.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
run_admixture(
  bed,
  Reps = 2,
  Kvals = 2:5,
  path = ".",
  outdir = "admixture_runs",
  num_cores = max(1, parallel::detectCores() - 1),
  use_existing_directory = FALSE,
  more_flags = ""
)

Arguments

bed

the bed file to use. (With the .bed extension. Example = "plink.bed".) The .bim file has to be with it in the same directory as well as the .fam file. These three files will both get copied to "input.bed" and "input.bim" in the "data" directory in the outdir

Reps

number or reps to do

Kvals

vector of K-values to use

path

the path that gets you to the directory you want to put all the results in.

outdir

the single name of the output directory you want

num_cores

the number of cores to parallelize the admixture runs over. By default it will try to detect the number of cores and then use 1 less than that. (or 1, whichever is larger). But you can set it to whatever...

use_existing_directory

If you want to place files into an existing outdir without throwing an error, set this to TRUE

more_flags

any additional flags to run admixture with


eriqande/genoscapeRtools documentation built on Dec. 27, 2021, 8:01 a.m.