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Write a structure file from a tidy data frame

Source: R/write_structure.R
write_structure.Rd

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

Usage

write_structure(data, pop.levels = 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.

pop.levels

(optional, string) This refers to the levels in a factor. In this case, the id of the pop. Use this argument to have the pop ordered your way instead of the default alphabetical or numerical order. e.g. pop.levels = c("QUE", "ONT", "ALB") instead of the default pop.levels = c("ALB", "ONT", "QUE"). White spaces in population names are replaced by underscore. Default: pop.levels = NULL.

filename

(optional) The file name prefix for the structure file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_structure_. Default: filename = NULL.

...

other parameters passed to the function.

Value

A structure 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

Pritchard JK, Stephens M, Donnelly P. (2000) Inference of population structure using multilocus genotype data. Genetics. Genetics Society of America. 155: 945–959.

Author

Thierry Gosselin thierrygosselin@icloud.com