genind_to_genepop: Convert a genind object into a GENEPOP file

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Convert a genind object into a GENEPOP file

Description

The function converts an object of class genind into a GENEPOP file. It then allows to use the functionalities of the GENEPOP software and its derived package GENEPOP on R, as well as some functions from other packages (differentiation test, F-stats calculations, HWE test,...). 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_genepop(x, output = "data.frame")

Arguments

x

An object of class genind from package adegenet.

output

A character string indicating the option used to select what the function will return: If output = "data.frame"(default), then the function will return an object 'x' of class data.frame ready to be saved as a text file with the following command: write.table(x, file = "file_name.txt", quote=FALSE, row.names=FALSE, col.names=FALSE) If 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 GENEPOP software.

Value

An object of type data.frame if ouput = "data.frame". 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

Confusion

Do not confound this function with genind2genpop from adegenet. The latter converts an object of class genind into an object of class genpop, whereas genind_to_genepop converts an object of class genind into a text file compatible with GENEPOP software (Rousset, 2008).

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

References

\insertRef

raymond1995genepopgraph4lg

See Also

For more details about GENEPOP file formatting : https://genepop.curtin.edu.au:443/help_input.html. For the opposite conversion, see genepop_to_genind. The output file can be used to compute pairwise FST matrix with mat_pw_fst

Examples

data(data_ex_genind)
x <- data_ex_genind
df_genepop <- suppressWarnings(genind_to_genepop(x,
                                                 output = "data.frame"))

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