genind_to_structure: Convert a genind object into a STRUCTURE file

In graph4lg: Build Graphs for Landscape Genetics Analysis

Convert a genind object into a STRUCTURE file

Description

The function converts an object of class genind into a STRUCTURE file. It is designed to be used with diploid microsatellite data with alleles coded with 2 or 3 digits or SNPs genind objects.

Usage

genind_to_structure(x, output = "")

Arguments

x	An object of class genind from package adegenet.
output	A character string of the form output = "path_to_file/file_name.txt". Then, the function will write a text file named 'file_name.txt' in the directory corresponding to 'path_to_file'. Without 'path_to_file', the text file is written in the current working directory. The text file has the format required by STRUCTURE software.

Value

If output is the path and/or the file name of a text file, then nothing is returned in R environment but a text file is created with the specified file name, either in the current working directory or in the specified folder.

Warning

Allele coding

This function can handle genetic data with different allele coding: 2 or 3 digit coding for microsatellite data or 2 digit coding for SNPs (A,C,T,G become respectively 01, 02, 03, 04).

Individuals order

When individuals in input data are not ordered by populations, individuals from the same population can be separated by individuals from other populations. It can be problematic when calculating then pairwise distance matrices. Therefore, in such a case, individuals are ordered by populations and populations ordered in alphabetic order.

Author(s)

P. Savary

Examples

data(data_ex_genind)
x <- data_ex_genind
genind_to_structure(x,
                    output = tempfile(fileext = ".txt"))

graph4lg documentation built on Feb. 16, 2023, 5:43 p.m.