write_to_structure: Take simulated genotypes and write to a STRUCTURE input file...

In danwkenn/SimAdmixtR: Simulates a set of admixed diploid genotypes based on SNP allele frequencies

Description

Take simulated genotypes and write to a STRUCTURE input file format.

Usage

write_to_structure(
  sim_data,
  structure_snp_order = NULL,
  example_structure_file = NULL,
  sample_names = NULL,
  output = "test",
  type = c("txt", "csv"),
  keep_extra_snps = TRUE
)

Arguments

sim_data	Output from simulate_admixture
structure_snp_order	(Optional) The desired order of SNPs for columns of output file.
example_structure_file	(Optional) A sample STRUCTURE input file to extract the desired order of SNPs from. If both example_structure_file and structure_snp_order are specified, the order given by this will take precedence.
sample_names	(Optional) vector of names for the simulated samples.
output	Name for the output file.
type	Options for txt or csv file outputs.
keep_extra_snps	If there are SNPs present in the simulated data, but not in the SNP order provided by example_structure_file or structure_snp_order, should the extra SNPs be kept and appended to the table (on the right)?

Value

NULL

Examples

#Download files to temporary directory:
temp_dir <- tempdir()
download.file(url = "https://raw.githubusercontent.com/danwkenn/SimAdmixtR/master/inst/example-files/input-allele-frequencies-three-snps.csv",destfile = paste0(temp_dir,"/input-af-example.csv"))
download.file(url = "https://raw.githubusercontent.com/danwkenn/SimAdmixtR/master/inst/example-files/simple-three-allele-example.csv",destfile = paste0(temp_dir,"/example-structure-file.csv"))

sim_data <- simulate_admixture(
n_samples = 10,
ancestor_pop_label = c(1,2,2,2),
file = paste0(temp_dir,"/input-af-example.csv")
)

write_to_structure(
sim_data = sim_data,
example_structure_file = paste0(temp_dir,"/example-structure-file.csv"),
output = "example-output",
type = c("txt","csv"))

danwkenn/SimAdmixtR documentation built on May 30, 2020, 7:25 a.m.