protti: fetch_uniprot_proteome – R documentation

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fetch_uniprot_proteome

Fetch proteome data from UniProt

Fetches proteome data from UniProt for the provided organism ID.

fetch_uniprot_proteome(organism_id, columns = c("id"), reviewed = TRUE)

`organism_id`	a numeric vector of one NCBI taxonomy identifier (TaxId) for and organism of choice.
`columns`	a character vector of metadata columns that should be imported from UniProt (all possible columns can be found here: https://www.uniprot.org/help/uniprotkb_column_names). 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. If true, only reviewed protein entries will be retrieved.

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

head(fetch_uniprot_proteome(9606))

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

v0.1.1

MIT + file LICENSE

Authors

Jan-Philipp Quast [aut, cre], Dina Schuster [aut], ETH Zurich [cph, fnd]

Initial release