Update the backing matrix — gt_update_backingfile • tidypopgen

This functions forces a re-write of the file backing matrix to match the gen_tibble. Individuals and loci are subsetted and reordered according to the current state of the gen_tibble. Tests for this function are in test_gt_order_loci.R

Usage

gt_update_backingfile(
  .x,
  backingfile = NULL,
  chunk_size = NULL,
  ignore_genetic_dist = TRUE,
  quiet = FALSE
)

Arguments

.x: a gen_tibble object
backingfile: @param 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 left to NULL (the default), the file name will be based on the name f the current backing file.
chunk_size: the number of loci to process at once
ignore_genetic_dist: boolean to ignore the genetic distance when checking. Note that, if gentic_dist are being ignored and they are not sorted, the function will set them to zero to avoid problems with other software.
quiet: boolean to suppress information about the files

Value

a gen_tibble with a backing file (i.e. a new File Backed Matrix)