Run STRUCTURE in current path

Share:

Description

Run STRUCTURE in current path

Usage

1
2
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

1
2
3
4
5
6
7
## 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)