Order the loci table of a gen_tibble — gt_order

This function reorders the loci table so that positions within a chromosome are sequential. It also re-saves the genotypes into a new file backed matrix with the new order, so that it can be used by functions such as loci_ld_clump() and gt_pca_autoSVD(). If the loci table is already ordered, the original gen_tibble is returned.

Usage

gt_order_loci(
  .x,
  use_current_table = FALSE,
  ignore_genetic_dist = TRUE,
  quiet = FALSE,
  ...
)

Arguments

.x: a gen_tibble
use_current_table: boolean, if FALSE (the default), the table will be reordered; if TRUE, then the current loci table, which might have been reordered manually, will be used, but only if the positions within each chromosome are sequential
ignore_genetic_dist: boolean to ignore the genetic distance when checking. Note that, if genetic_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
...: other arguments

Value

A gen_tibble

Examples

example_gt <- example_gt("gen_tbl") %>% select_loci(c(1, 5, 2, 6, 4, 3))

# Loci are in the wrong order
show_loci(example_gt)
#> # A tibble: 6 × 8
#>   big_index name  chromosome position genetic_dist allele_ref allele_alt chr_int
#>       <int> <chr> <chr>         <int>        <dbl> <chr>      <chr>        <int>
#> 1         1 rs1   chr1              3            0 A          T                1
#> 2         5 rs5   chr2             23            0 C          G                2
#> 3         2 rs2   chr1              5            0 T          C                1
#> 4         6 rs6   chr2            456            0 T          A                2
#> 5         4 rs4   chr1            343            0 G          C                1
#> 6         3 rs3   chr1             65            0 C          NA               1

# Reorder the loci, ignoring genetic distance
example_gt_ordered <- gt_order_loci(example_gt, ignore_genetic_dist = TRUE)
#> Genetic distances are not sorted, setting them to zero
#> 
#> gen_backing files updated, now
#> using bigSNP file: /tmp/RtmpyN1xne/file22a251b9e08f_v2.rds
#> with backing file: /tmp/RtmpyN1xne/file22a251b9e08f_v2.bk
#> make sure that you do NOT delete those files!

# Loci are now in the correct order
show_loci(example_gt_ordered)
#> # A tibble: 6 × 8
#>   big_index name  chromosome position genetic_dist allele_ref allele_alt chr_int
#>       <int> <chr> <chr>         <int>        <dbl> <chr>      <chr>        <int>
#> 1         1 rs1   chr1              3            0 A          T                1
#> 2         2 rs2   chr1              5            0 T          C                1
#> 3         3 rs3   chr1             65            0 C          NA               1
#> 4         4 rs4   chr1            343            0 G          C                1
#> 5         5 rs5   chr2             23            0 C          G                2
#> 6         6 rs6   chr2            456            0 T          A                2