query_uniprot {queryup}

Retrieve data from UniProt using UniProt's REST API.

Description

Retrieve data from UniProt using UniProt's REST API. To avoid non-responsive queries, they are split into smaller queries with at most max_keys items per query field. Not that it works only with queries where items within query fields are collapsed with '+OR+' and different query fields are collapsed with '+AND+' (see query_uniprot())

Usage

query_uniprot(
  query = NULL,
  base_url = "https://rest.uniprot.org/uniprotkb/",
  columns = c("accession", "id", "gene_names", "organism_id", "reviewed"),
  max_keys = 200,
  updateProgress = NULL,
  show_progress = TRUE
)

Arguments

query

list of keys corresponding to UniProt's query fields. For example : query = list("gene_exact" = c("Pik3r1", "Pik3r2"), "organism_id" = c("10090", "9606"), "reviewed" = "true"). See 'query_fields' for available query fields.

base_url

The base url for the UniProt REST API

columns

names of UniProt data columns to retrieve. Examples include "accession", "id", "genes", "keywords", "sequence". See 'return_fields' for available return fields.

max_keys

maximum number of field items submitted

updateProgress

used to display progress in shiny apps

show_progress

Show progress bar

Value

a data.frame

Examples

# Get the UniProt entries of all proteins encoded by gene Pik3r1
ids <- c("P22682", "P47941")
query = list("accession_id" = ids)
df <-  query_uniprot(query = query)
head(df)