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

Source: R/genind.R

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

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

Arguments

data

(4 options) A file or object generated by radiator:

  • tidy data

  • Genomic Data Structure (GDS)

How to get GDS and tidy data ? Look into tidy_genomic_data, read_vcf or tidy_vcf.

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

(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

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