Read a genlight object into a tidy data frame and/or GDS object/file

Read a genlight object into a tidy data frame and/or GDS object/file. Used internally in genometranslator and might be of interest for users.

Usage

read_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: Logical indicating whether progress messages are emitted. Default: verbose = FALSE.
parallel.core: Number of workers available for parallel operations. Default: parallel.core = parallel::detectCores() - 1.

Details

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 ncol(genlight) will be integrated in the tidy dataset.
is.null(data@position): an integer string of length = ncol(genlight) will be integrated in the tidy dataset.

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

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 genlight objects requires the optional CRAN package adegenet.

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