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Write a related file from a tidy data frame

Source: R/write_related.R
write_related.Rd

Write a related file from a tidy data frame. This output file format enables to run the data in the related R package (Pew et al. 2015), which is essantially the R version of COANCESTRY fortran program developed by Jinliang Wang. Used internally in genometranslator and might be of interest for users.

Usage

write_related(
  data,
  filename = NULL,
  parallel.core = parallel::detectCores() - 1,
  ...
)

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 the related file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_related_. Default: filename = NULL.

parallel.core

Default: parallel.core = parallel::detectCores() - 1.

...

other parameters passed to the function.

Value

A related 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

Pew J, Muir PH, Wang J, Frasier TR (2015) related: an R package for analysing pairwise relatedness from codominant molecular markers. Molecular Ecology Resources, 15, 557-561.

Wang, J. 2011. COANCESTRY: A program for simulating, estimating and analysing relatedness and inbreeding coefficients. Molecular Ecology Resources 11(1): 141-145.

Author

Thierry Gosselin thierrygosselin@icloud.com