Convert a GDS genome to a tidy table — tidy

Materialize selected individuals and markers from a GDS file or open GDS object as a tidy genomic table.

Usage

tidy_genome(
  data,
  markers.meta = NULL,
  markers.meta.select = NULL,
  wide = FALSE,
  individuals = NULL,
  pop.id = FALSE,
  calibrate.alleles = TRUE,
  strip.rad = FALSE,
  parallel.core = parallel::detectCores() - 1,
  close.gds = FALSE,
  ...
)

Arguments

data: A GDS filename or open SeqVarGDSClass object.
markers.meta: Default: markers.meta = NULL.
markers.meta.select: Default: markers.meta.select = NULL.
wide: Default: wide = FALSE.
individuals: Default: individuals = NULL.
pop.id: Logical. When pop.id = TRUE, the strata column is named POP_ID; otherwise it is named STRATA. Default: pop.id = FALSE.
calibrate.alleles: Default: calibrate.alleles = TRUE.
strip.rad: Default: strip.rad = FALSE.
parallel.core: Default: parallel.core = parallel::detectCores() - 1.
close.gds: Logical. Close an open GDS object supplied by the caller. A GDS opened internally from a filename is always closed. Default: close.gds = FALSE.

Value

A tidy genomic data frame.