Write a fineRADstructure file from a tidy data frame

Write a fineRADstructure file from a tidy data frame. Used internally in genometranslator and might be of interest for users.

Usage

write_fineradstructure(data, strata = NULL, filename = NULL)

Arguments

data: A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into genometranslator tidy_genome.
strata: (path or object) The strata file or object. Additional documentation is available in read_strata. Use that function to whitelist/blacklist populations/individuals. Option to set pop.levels/pop.labels is also available. Default: strata = NULL.
filename: (optional) The file name prefix for the fineRADstructure file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_fineradstructure_. Default: filename = NULL.

Value

A fineRADstructure file is written in the working directory. An object is also returned in the global environment.

Details

fineRADstructure requires special formating for populations, it needs to be ONLY LETTERS, not numbers. This information is then merged with the sample id (converted to integers). radiator will generate a dictionary file.

Life cycle

It become increasingly difficult for me to follow all the different naming schemes researcher uses, if they're is any strategy... Consequently, I have abandoned the idea of formating with letters the populations to generate the fineRADstrucure file. If you get an error see the the details section.

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

Malinsky, M., Trucchi, E., Lawson, D., Falush, D. (2018). RADpainter and fineRADstructure: population inference from RADseq data. Mol. Biol. Evol. 35(5), 1284-1290. https://dx.doi.org/10.1093/molbev/msy023

Author

Thierry Gosselin thierrygosselin@icloud.com