Convert a single-locus table to STAVE-style variant identifiers — convert_single_locus_table_to

Builds a variant column by concatenating gene_id, aa_position, and aa as gene_id:aa_position:aa, then returns variant plus any requested additional columns.

Usage

convert_single_locus_table_to_stave(df, additional_columns = NULL)

Arguments

df: A data frame with columns gene_id, aa_position, and aa, plus any columns named in additional_columns.
additional_columns: Optional character vector of extra columns to keep.

Value

A data frame with a variant column and any additional_columns.

Examples

df <- data.frame(
  gene_id = c("PF3D7_0417200.1", "PF3D7_0417200.1"),
  aa_position = c(51, 59),
  aa = c("I", "R"),
  prev = c(0.5, 1)
)
convert_single_locus_table_to_stave(df, additional_columns = "prev")
#>                variant prev
#> 1 PF3D7_0417200.1:51:I  0.5
#> 2 PF3D7_0417200.1:59:R  1.0