fetch_uniprot: Fetch protein data from UniProt

In protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Fetch protein data from UniProt

Description

Fetches protein metadata from UniProt.

Usage

fetch_uniprot(
  uniprot_ids,
  columns = c("protein_name", "length", "sequence", "gene_names", "xref_geneid",
    "xref_string", "go_f", "go_p", "go_c", "cc_interaction", "ft_act_site", "ft_binding",
    "cc_cofactor", "cc_catalytic_activity", "xref_pdb"),
  batchsize = 200,
  show_progress = TRUE
)

Arguments

uniprot_ids	a character vector of UniProt accession numbers.
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")
batchsize	a numeric value that specifies the number of proteins processed in a single single query. Default and max value is 200.
show_progress	a logical value that determines if a progress bar will be shown. Default is TRUE.

Value

A data frame that contains all protein metadata specified in columns for the proteins provided. If an invalid ID was provided that contains a valid UniProt ID, the valid portion of the ID is fetched and the invalid input ID is saved in a column called input_id.

Examples

fetch_uniprot(c("P36578", "O43324", "Q00796"))

protti documentation built on Jan. 22, 2023, 1:11 a.m.