runStructure: Run STRUCTURE in current path

In starmie: Population Structure Model Inference and Visualisation

Description

Run STRUCTURE in current path

Usage

runStructure(path_to_structure, input_file, main_params, extra_params,
  out_prefix, n_K, n_replicates, n_cores)

Arguments

path_to_structure	path to structure binary executable (ie. /usr/bin/structure)
input_file	file name of input data
main_params	file name of mainparams file for STRUCTURE
extra_params	file name of extraparams file for STRUCTURE
out_prefix	prefix path/name for logging
n_K	number of assumed populations to try
n_replicates	number of replicates
n_cores	number of cores

Note

Set RANDOMIZE = 0 in main params file to avoid using same seed. Haven't tested on Windows.

Examples

## Not run: 
input_file <- system.file("inst/extdata/microsat_testfiles", "locprior.str", package = "starmie")
main_params <- system.file("inst/extdata/microsat_testfiles", "mainparams", package = "starmie")
extra_params <-  system.file("inst/extdata/microsat_testfiles", "extraparams", package = "starmie")
runStructure("structure", input_file, main_params, extra_params, "test", 5, 2, 2)

## End(Not run)

starmie documentation built on May 1, 2019, 8:01 p.m.