Write a genind object from a tidy data frame or GDS file or object.

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

Usage

write_genind(data, write = FALSE, verbose = FALSE)

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 genind object. The file is written with radiator_genind_DATE@TIME.RData and can be open with load or readRDS. Default: write = FALSE.
verbose: Logical indicating whether progress messages are emitted. Default: verbose = FALSE.

Dependencies

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

Reading and writing genind objects requires the optional CRAN package adegenet.

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

Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 1403-1405.

Jombart T, Ahmed I (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics, 27, 3070-3071.

Author

Thierry Gosselin thierrygosselin@icloud.com