Write a strataG gtypes object from GDS or tidy data

Write a strataG object from a tidy data frame. Used internally in genometranslator and might be of interest for users.

Usage

write_gtypes(data, write = FALSE, filename = NULL)

Arguments

data: A supported genomic file, object, or tidy genomic data frame. Default: data = NULL.
write: (logical, optional) To write in the working directory the gtypes object. The file is written with radiator_gtypes_DATE@TIME.RData if no filename is provided and can be open with load or readRDS. Default: write = FALSE.
filename: (character, optional) Filename prefix. Default: filename = NULL.

Value

An object of the class strataG is returned.

Dependencies

Required package dependencies are declared in DESCRIPTION and installed with genometranslator. Run genometranslator_dependencies() to inspect core packages, optional packages, and external executables.

gtypes support requires the optional GitHub package strataG. Consult its repository for current installation and troubleshooting information.

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.

References

Archer FI, Adams PE, Schneiders BB. strataG: An r package for manipulating, summarizing and analysing population genetic data. Molecular Ecology Resources. 2017; 17: 5-11. doi:10.1111/1755-0998.12559

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
# require(strataG)
# with radiator GDS
turtle <- genometranslator::write_gtypes(data = "my.metadata.node.rad")

# with tidy data
turtle <- genometranslator::write_gtypes(data = "my.radiator.rad")
} # }