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Write a genepop file

Source: R/genepop.R
write_genepop.Rd

Write a genepop file from a tidy data frame or GDS file/object. Used internally in genometranslator 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

A supported genomic file, object, or tidy genomic data frame. Default: data = NULL.

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. With the default, Will use "radiator genepop with date". Default: genepop.header = NULL.

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_. Default: filename = NULL.

...

other parameters passed to the function.

Value

A genepop file is saved to the working directory.

Data filtering

This writer does not silently filter markers or individuals. It may validate requirements imposed by the destination format and stop with an informative error when the input is unsuitable. It is the user's responsibility to filter and quality-control the data appropriately for the intended analysis before generating the output. Use radr or another suitable workflow when filtering is required.

Dependencies

Required package dependencies are declared in DESCRIPTION and are installed with genometranslator. Any additional dependency needed only for this format or option is identified in this help page. Use genometranslator_dependencies() to inspect the availability of core packages, optional packages, and external executables.

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

Author

Thierry Gosselin thierrygosselin@icloud.com