Retrieve gene synonyms

Given a list of genes (id, name, bnumber or gi), get the gene synonyms (name, bnumber of gi).

get_gene_synonyms(
  regulondb,
  genes,
  from = "name",
  to = c("id", "name", "bnumber", "gi")
)

Arguments

regulondb

A regulondb() object.

genes

Character vector of gene identifiers (id, name, bnumber or gi).

from

A character() specifying one of: id, name, bnumber of gi

to

A character() specifying one or more of: id, name, bnumber of gi

Value

A regulondb_result object.

Author

Jesús Emiliano Sotelo Fonseca

Examples

## Connect to the RegulonDB database if necessary
if (!exists("regulondb_conn")) regulondb_conn <- connect_database()

## Build the regulon db object
e_coli_regulondb <-
    regulondb(
        database_conn = regulondb_conn,
        organism = "E.coli",
        database_version = "1",
        genome_version = "1"
    )

## Lists all available identifiers for "araC"
get_gene_synonyms(e_coli_regulondb, "araC", from = "name")
#> regulondb_result with 1 row and 4 columns
#>             id        name     bnumber          gi
#>    <character> <character> <character> <character>
#> 1 ECK120000050        araC       b0064          NA

## Retrieve only the ID
get_gene_synonyms(e_coli_regulondb, "araC", from = "name", to = "id")
#> regulondb_result with 1 row and 1 column
#>             id
#>    <character>
#> 1 ECK120000050

## Use an ID to retrieve the synonyms
get_gene_synonyms(e_coli_regulondb, "ECK120000998", from = "id")
#> regulondb_result with 1 row and 4 columns
#>             id        name     bnumber          gi
#>    <character> <character> <character> <character>
#> 1 ECK120000998        tolC       b3035          NA