Tidy a genlight object to a tidy dataframe and/or GDS object/file

Tidy genlight object to a tidy dataframe and/or GDS object/file. Used internally in radiator and might be of interest for users.

tidy_genlight(
  data,
  tidy = TRUE,
  gds = TRUE,
  write = FALSE,
  verbose = FALSE,
  parallel.core = parallel::detectCores() - 1
)

Arguments

data: (path or object) A genlight object in the global environment or path to a genlight file that will be open with readRDS.
tidy: (logical) Generate a tidy dataset. Default: tidy = TRUE.
gds: (optional, logical) To write a radiator gds object. Default: gds = TRUE.
write: (optional, logical) To write in the working directory the tidy data. The file is written with radiator_genlight_DATE@TIME.rad. Default: write = FALSE.
verbose: (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.
parallel.core: (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

A string of the same dimension is generated when genlight:

is.null(genlight@pop): pop will be integrated in the tidy dataset.
is.null(data@chromosome): CHROM1 will be integrated in the tidy dataset.
is.null(data@loc.names): LOCUS1 to dim(genlight)[2] will be integrated in the tidy dataset.
is.null(data@position): an integer string of length = dim(genlight)[2] will be integrated in the tidy dataset.

Note: that if all CHROM, LOCUS and POS is missing the function will be terminated

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.