Fetch proteome data from UniProt

Fetches proteome data from UniProt for the provided organism ID.

fetch_uniprot_proteome(
  organism_id,
  columns = c("accession"),
  reviewed = TRUE,
  timeout = 120,
  max_tries = 5
)

Arguments

organism_id

a numeric value that specifies the NCBI taxonomy identifier (TaxId) for an organism.

columns

a character vector of metadata columns that should be imported from UniProt (all possible columns can be found here. For cross-referenced database provide the database name with the prefix "xref_", e.g. "xref_pdb"). Note: Not more than one or two columns should be selected otherwise the function will not be able to efficiently retrieve the information. If more information is needed, fetch_uniprot() can be used with the IDs retrieved by this function.

reviewed

a logical value that determines if only reviewed protein entries will be retrieved.

timeout

a numeric value specifying the time in seconds until the download times out. The default is 60 seconds.

max_tries

a numeric value that specifies the number of times the function tries to download the data in case an error occurs. The default is 2.

Value

A data frame that contains all protein metadata specified in columns for the organism of choice.

Examples

# \donttest{
head(fetch_uniprot_proteome(9606))
#> # A tibble: 6 × 1
#>   accession 
#>   <chr>     
#> 1 A0A087X1C5
#> 2 A0A0B4J2F0
#> 3 A0A0B4J2F2
#> 4 A0A0C5B5G6
#> 5 A0A0K2S4Q6
#> 6 A0A0U1RRE5
# }