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List species metadata present in OrthoMCL

Source: R/listOrthomcl.R
listOrthomcl.Rd

A convenience function to quickly fetch the species related vocabulary of ≥ 857 species used by OrthoMCL database. This function helps users choose numeric IDs of the organisms between which they wish to fetch the paired orthologs. See also: getpairedOrthologs().

Usage

listOrthomcl(api_key = Sys.getenv("VEUPATHDB_API_KEY"))

Arguments

api_key

Character. VEuPathDB API key used for authentication. By default, the value is obtained from the VEUPATHDB_API_KEY environment variable.

Value

A data frame containing information about species present in OrthoMCL and their database associated ID.

Details

User should note that the numeric IDs used by OrthoMCL are not stable and changes upon every update. So an ID which was previously assigned to Plasmodium falciparum 3D7 might get assigned to a new organism in new release. Therefore users are encouraged to run this function prior to running of getpairedOrthologs()

Examples

if (FALSE) { # \dontrun{
listOrthomcl()
} # }