write_genepop: Write a genepop file

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Write a genepop file

Description

Write a genepop file from a tidy data frame or GDS file/object. Used internally in radiator and assigner and might be of interest for users.

Usage

write_genepop(
  data,
  pop.levels = NULL,
  genepop.header = NULL,
  markers.line = TRUE,
  filename = NULL,
  ...
)

Arguments

data	(4 options) A file or object generated by radiator: tidy data Genomic Data Structure (GDS) How to get GDS and tidy data ? Look into tidy_genomic_data, read_vcf or tidy_vcf.
pop.levels	(optional, string) A character string with your populations ordered. Default: pop.levels = NULL. Described in read_strata.
genepop.header	The first line of the Genepop file. Default: genepop.header = NULL will use "radiator genepop with date".
markers.line	(optional, logical) In the genepop and structure file, you can write the markers on a single line separated by commas markers.line = TRUE, or have markers on a separate line, i.e. in one column, for the genepop file (not very useful with thousands of markers) and not printed at all for the structure file. Default: markers.line = TRUE.
filename	(optional) The file name prefix for the genepop file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_genepop_.
...	other parameters passed to the function.

Value

A genepop file is saved to the working directory.

Author(s)

Thierry Gosselin [e-mail]

References

Raymond M. & Rousset F, (1995). GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Heredity, 86:248-249

Rousset F. genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources. 2008, 8: 103-106. doi:10.1111/j.1471-8286.2007.01931.x

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.