fetch_uniprot_proteome: Fetch proteome data from UniProt

In 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)

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.

Value

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

Examples

head(fetch_uniprot_proteome(9606))

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