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Find duplicates in the loci table

Source: R/is_loci_table_ordered.R
find_duplicated_loci.Rd

This function finds duplicated SNPs by checking the positions within each chromosome. It can return a list of duplicated SNPs or a logical value indicating whether there are any duplicated loci.

Usage

find_duplicated_loci(.x, error_on_false = FALSE, list_duplicates = TRUE, ...)

Arguments

.x

a vector of class vctrs_bigSNP (usually the genotype column of a gen_tibble object), or a gen_tibble.

error_on_false

logical, if TRUE an error is thrown if duplicated loci are found.

list_duplicates

logical, if TRUE returns duplicated SNP names.

...

other arguments passed to specific methods.

Value

If list_duplicates is TRUE, returns a character vector of duplicated loci names (character(0) when none). If list_duplicates is FALSE, returns TRUE when no duplicates exist and FALSE when duplicates are present. If error_on_false is TRUE and duplicates exist, an error is thrown.

Examples

example_gt <- load_example_gt("gen_tbl")
show_loci(example_gt) <- test_loci <- data.frame(
  big_index = c(1:6),
  name = paste0("rs", 1:6),
  chromosome = paste0("chr", c(1, 1, 1, 1, 1, 1)),
  position = as.integer(c(3, 3, 5, 65, 343, 46)),
  genetic_dist = as.double(rep(0, 6)),
  allele_ref = c("A", "T", "C", "G", "C", "T"),
  allele_alt = c("T", "C", NA, "C", "G", "A")
)

show_loci(example_gt)
#> # A tibble: 6 × 7
#>   big_index name  chromosome position genetic_dist allele_ref allele_alt
#>       <int> <chr> <fct>         <int>        <dbl> <chr>      <chr>     
#> 1         1 rs1   chr1              3            0 A          T         
#> 2         2 rs2   chr1              3            0 T          C         
#> 3         3 rs3   chr1              5            0 C          NA        
#> 4         4 rs4   chr1             65            0 G          C         
#> 5         5 rs5   chr1            343            0 C          G         
#> 6         6 rs6   chr1             46            0 T          A         

# Find which loci are duplicated
example_gt %>% find_duplicated_loci()
#> [1] "rs1" "rs2"