fetch_uniprot_proteome: Fetch proteome data from UniProt

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

Fetch proteome data from UniProt

Description

Fetches proteome data from UniProt for the provided organism ID.

Usage

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

head(fetch_uniprot_proteome(9606))

jpquast/protti documentation built on Oct. 23, 2024, 4:59 a.m.