Write a plink tped/tfam file from a tidy data frame — write

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

Usage

write_plink(data, 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.
filename: (optional) The file name prefix for tped/tfam files written to the working directory. With default: filename = NULL, the date and time is appended to radiator_plink_. Default: filename = NULL.

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

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics. 2007: 81: 559–575. doi:10.1086/519795

Author

Thierry Gosselin thierrygosselin@icloud.com