Convert Other IDs to Ensembl gene IDs

A convenience function to quickly convert the Uniprot or Entrez Ids to Ensembl gene IDs, using VEuPathDB specialized databases.It also provides description and gene symbol for input Ids.

Usage

toGeneid(
  inputid,
  from = "",
  to = "",
  org = "Plasmodium falciparum 3D7",
  db = "plasmodb",
  ...
)

Arguments

inputid

A character vector of IDs. Can be Ensembl, Uniprot, Entrez or or old Pf ids.

from

To describe the type of Input ID. Possible values: "old", "uniprot". "entrez", "ensembl"

to

To describle the type of output ID desired. Possible values: "emsembl".

org

Organism to which the IDs belongs to.Possible values: toxodb, plasmodb, hostdb, amoebadb, cryptodb, fungidb, giardiadb, microsporidiadb, piroplasmadb, trichdb, tritrypdb.

db

Database in which organism is present.

...

Additional arguments that can be passed to the getTable() function.

Value

A data frame, containing Gene IDs, gene description and gene Symbols and more.

Details

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{
df <- toGeneid(
c("PF3D7_0420300", "PF3D7_0621000"),
      from="ensembl",api_key=Sys.getenv("VEUPATHDB_API_KEY"))
} # }