Convert identifiers from one type to another

Converts between current gene IDs, previous gene IDs, UniProt IDs and Entrez IDs using getTableVeupathdb(). All possible combinations are allowed.

Usage

toGeneid(
  inputid,
  from = "",
  to = "ensembl",
  api_key = Sys.getenv("VEUPATHDB_API_KEY")
)

Arguments

inputid

Character vector of identifiers to convert.Can be vector of mixed identifiers.

from

Input identifier type. One of "ensembl", "uniprot", "entrez" or "old".

to

Desired output identifier type. One of "ensembl", "uniprot", "entrez" or "old". Defaults to "ensembl".

api_key

VEuPathDB API key.

Value

A data frame containing Input ID, Output ID, Gene ID and Organism. Multiple mappings are returned as separate rows.

Details

Supports mixed-organism identifiers without requiring organism or database information.

All available gene-identifier associations are retained, including one-to-many and many-to-many mappings.

With release 71 of VEuPathDB, only users with subscription and API key can access the database programmatically. Use usethis::edit_r_environ(scope = "user") to add VEuPathDB API using VEUPATHDB_API_KEY variable.

Examples

if (FALSE) { # \dontrun{

# Gene IDs to UniProt IDs
df <- toGeneid(
  c("PF3D7_1372300", "PBANKA_1355600"),
  from = "ensembl",
  to = "uniprot"
)

# UniProt IDs to gene IDs
df <- toGeneid(
  c("A0A509APC6", "Q75UY1"),
  from = "uniprot",
  to = "ensembl"
)

# Previous IDs to UniProt IDs
df <- toGeneid(
  "PBANKA_135560",
  from = "old",
  to = "uniprot"
)
} # }