tidypopgen (version 0.4.3)

select_loci: The select verb for loci

Description

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.

Usage

select_loci(.data, .sel_arg)

Value

a gen_tibble with a subset of the loci.

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.

See Also

dplyr::select()

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)

# Select loci by index
example_gt_subset <- example_gt %>% select_loci(all_of(c(4, 2, 1)))
show_loci(example_gt_subset)