Map a variant id to an EFO trait — variant_to

Map a variant identifier to an EFO trait identifier. Variants are first mapped to association identifiers, and then to EFO traits. Set the option keep_association_id to TRUE to keep the intermediate mapping, i.e., the association identifiers.

Usage

variant_to_trait(
  variant_id,
  keep_association_id = FALSE,
  verbose = FALSE,
  warnings = TRUE
)

Arguments

variant_id: A character vector of variant identifiers.
keep_association_id: Whether to keep the association identifier in the final output (default is FALSE).
verbose: Whether the function should be verbose about the different queries or not.
warnings: Whether to print warnings.

Value

A dataframe of two or three identifiers. If

keep_association_id is set to FALSE, the first column is the variant identifier and the second column is the EFO trait identifier, otherwise the variable association_id is also included as the second column.

Examples

if (FALSE) {
# Map GWAS variant identifiers to EFO trait identifiers
variant_to_trait(c('rs7904579', 'rs138331350'))

# Map GWAS variant identifiers to EFO trait identifiers
# but keep the intermediate association identifier
variant_to_trait(c('rs7904579', 'rs138331350'), keep_association_id = TRUE)
}