The select_if verb for loci

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.

Value

a subset of the list of loci in the gen_tibble

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.

Examples

example_gt <- 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)
#> # A tibble: 2 × 8
#>   big_index name  chromosome position genetic_dist allele_ref allele_alt chr_int
#>       <int> <chr> <chr>         <int>        <dbl> <chr>      <chr>        <int>
#> 1         5 rs5   chr2             23            0 C          G                2
#> 2         6 rs6   chr2            456            0 T          A                2

# Select loci by a summary statistic
example_gt_subset <- example_gt %>%
  select_loci_if(loci_maf(genotypes) > 0.2)
show_loci(example_gt_subset)
#> # A tibble: 5 × 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         4 rs4   chr1            343            0 G          C                1
#> 4         5 rs5   chr2             23            0 C          G                2
#> 5         6 rs6   chr2            456            0 T          A                2