write_fineradstructure: Write a fineRADstructure file from a tidy data frame

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

Write a fineRADstructure file from a tidy data frame

Description

Write a fineRADstructure file from a tidy data frame. Used internally in radiator 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 radiator tidy_genomic_data.
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.
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_.

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.

Value

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

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.

Author(s)

Thierry Gosselin [e-mail]

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

See Also

fineRADstructure

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