select_loci_if: The 'select_if' verb for 'loci'

In tidypopgen: Tidy Population Genetics

The select_if verb for loci

Description

An equivalent to dplyr::select_if() that works on the genotype column of a gen_tibble. This function has access to the genotypes (and thus can work on summary statistics to select), but not the names of the loci (look at select_loci() for that feature.

Usage

select_loci_if(.data, .sel_logical)

Arguments

.data	a gen_tibble
.sel_logical	a logical vector of length equal to the number of loci, or an expression that will tidy evaluate to such a vector. Only loci for which .sel_logical is TRUE will be selected; NA will be treated as FALSE.

Details

#' Note that the select_loci_if verb does not modify the backing FBM files, but rather it subsets the list of loci to be used stored in the gen_tibble.

Value

a subset of the list of loci in the gen_tibble

Examples

example_gt <- load_example_gt("gen_tbl")

# Select loci by chromosome
example_gt_subset <- example_gt %>%
  select_loci_if(loci_chromosomes(genotypes) == "chr2")
show_loci(example_gt_subset)

# Select loci by a summary statistic
example_gt_subset <- example_gt %>%
  select_loci_if(loci_maf(genotypes) > 0.2)
show_loci(example_gt_subset)

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