is_loci_table_ordered: Test if the loci table is ordered

In tidypopgen: Tidy Population Genetics

Test if the loci table is ordered

Description

This functions checks that all SNPs in a chromosome are adjacent in the loci table, and that positions are sorted within chromosomes.

Usage

is_loci_table_ordered(
  .x,
  error_on_false = FALSE,
  ignore_genetic_dist = TRUE,
  ...
)

## S3 method for class 'tbl_df'
is_loci_table_ordered(
  .x,
  error_on_false = FALSE,
  ignore_genetic_dist = TRUE,
  ...
)

## S3 method for class 'vctrs_bigSNP'
is_loci_table_ordered(
  .x,
  error_on_false = FALSE,
  ignore_genetic_dist = 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 the loci are not ordered.
ignore_genetic_dist	logical, if TRUE the physical position is not checked.
...	other arguments passed to specific methods.

Value

a logical vector defining which loci are transversions

Examples

example_gt <- load_example_gt("gen_tbl")

example_gt %>% is_loci_table_ordered()

tidypopgen documentation built on Aug. 28, 2025, 1:08 a.m.