R/write_fineradstructure.R
write_fineradstructure.RdWrite a fineRADstructure file from a tidy data frame. Used internally in radiator and might be of interest for users.
write_fineradstructure(data, strata = NULL, filename = NULL)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.
(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.
(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_.
A fineRADstructure file is written in the working directory. An object is also returned in the global environment.
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.
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.
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