tidypopgen (version 0.4.3)

gt_from_genlight: Convert a genlight object from adegenet to a gen_tibble

Description

This function converts a genlight object from the adegenet package to a gen_tibble object

Usage

gt_from_genlight(x, backingfile = NULL, ...)

Value

A gen_tibble object

Arguments

x

A genlight object

backingfile

the path, including the file name without extension, for backing files used to store the data (they will be given a .bk and .rds automatically). If NULL (default), backing files are placed in the temporary directory.

...

Additional arguments passed to gen_tibble().

Details

• Currently supports diploid genlight objects only (all values in @ploidy must be 2).

• Requires non-missing slots: loc.names, n.loc, loc.all, chromosome, position, ploidy, ind.names. The pop slot is optional; if absent, the returned gen_tibble will omit the population column.

Examples

if (FALSE) { # rlang::is_installed("adegenet")

# Create a simple genlight object
x <- new("genlight",
  list(
    indiv1 = c(1, 1, 0, 1, 1, 0),
    indiv2 = c(2, 1, 1, 0, 0, 0)
  ),
  ploidy = c(2, 2),
  loc.names = paste0("locus", 1:6),
  chromosome = c("chr1", "chr1", "chr2", "chr2", "chr3", "chr3"),
  position = c(100, 200, 150, 250, 300, 400),
  loc.all = c("A/T", "C/G", "G/C", "A/T", "T/C", "G/A"),
  pop = c("pop1", "pop2")
)


file <- paste0(tempfile(), "gt_from_genlight")
# Convert to gen_tibble
new_gt <- gt_from_genlight(x, backingfile = file)
}