An equivalent to dplyr::select() that works on the genotype column
of a gen_tibble, using the mini-grammar available for tidyselect. The
select-like evaluation only has access to the names of the loci (i.e. it
can select only based on names, not summary statistics of those loci; look
at select_loci_if() for that feature.
Arguments
- .data
a
gen_tibble- .sel_arg
one unquoted expression, using the mini-grammar of
dplyr::select()to select loci. Variable names can be used as if they were positions in the data frame, so expressions like x:y can be used to select a range of variables.
Details
Note that the select_loci 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 <- load_example_gt("gen_tbl")
# Select loci by name
example_gt_subset <- example_gt %>%
select_loci(all_of(c("rs1", "rs2", "rs3")))
show_loci(example_gt_subset)
#> # A tibble: 3 × 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 5 0 T C
#> 3 3 rs3 chr1 65 0 C NA
# Select loci by index
example_gt_subset <- example_gt %>% select_loci(all_of(c(4, 2, 1)))
show_loci(example_gt_subset)
#> # A tibble: 3 × 7
#> big_index name chromosome position genetic_dist allele_ref allele_alt
#> <int> <chr> <fct> <int> <dbl> <chr> <chr>
#> 1 4 rs4 chr1 343 0 G C
#> 2 2 rs2 chr1 5 0 T C
#> 3 1 rs1 chr1 3 0 A T