Update the backing matrix

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. A .gt, .bk and .rds file will be created.

Usage

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

Arguments

.x

a gen_tibble 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 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

rm_unsorted_dist

boolean to set genetic_dist to zero (i.e. remove it) if it is unsorted within the chromosomes.

quiet

boolean to suppress information about the files

Value

a gen_tibble with updated .gt, .bk, and .rds files (i.e. a new File Backed Matrix)

Details

This function does not check whether the positions of your genetic loci are sorted. To check this, and update the file backing matrix, use gt_order_loci(). Tests for this function are in test_gt_order_loci.R

Examples

example_gt <- load_example_gt("gen_tbl")

# Here, new backingfiles are created, but without using `<-` the object
# loaded in the R session is not updated
gt_update_backingfile(example_gt)
#> 
#> gen_backing files updated, now
#> using FBM RDS: /tmp/RtmpKZXfxT/file21802c0f09ee_v2.rds
#> with FBM backing file: /tmp/RtmpKZXfxT/file21802c0f09ee_v2.bk
#> make sure that you do NOT delete those files!
#> to reload the gen_tibble in another session, use:
#> gt_load('/tmp/RtmpKZXfxT/file21802c0f09ee_v2.gt')
#> # A gen_tibble: 6 loci
#> # A tibble:     7 × 3
#>   id    population  genotypes
#>   <chr> <chr>      <vctr_SNP>
#> 1 a     pop1        [1,1,...]
#> 2 b     pop1        [2,1,...]
#> 3 c     pop2        [2,.,...]
#> 4 d     pop2        [1,0,...]
#> 5 e     pop1        [1,2,...]
#> 6 f     pop3        [0,0,...]
#> 7 g     pop3        [0,1,...]

# Make sure to use `<-` to update the file names associated with the
# gen_tibble object loaded in the R session
example_gt <- example_gt %>% gt_update_backingfile()
#> 
#> gen_backing files updated, now
#> using FBM RDS: /tmp/RtmpKZXfxT/file21802c0f09ee_v3.rds
#> with FBM backing file: /tmp/RtmpKZXfxT/file21802c0f09ee_v3.bk
#> make sure that you do NOT delete those files!
#> to reload the gen_tibble in another session, use:
#> gt_load('/tmp/RtmpKZXfxT/file21802c0f09ee_v3.gt')