extract_names: Extract protein names into a list

In brennanpincardiff/drawProteins: Package to Draw Protein Schematics from Uniprot API output

Extract protein names into a list

Description

Extracts protein names from JSON object produced by a search of Uniprot with a single protein asking for all the information. The search produces a Large list that contains all the Uniprot information about a protein.

Usage

extract_names(protein_json)

Arguments

protein_json

A JSON object from a search with 14 primary parts

Value

A List of 6 with "accession", "name", "protein.recommendedName.fullName", gene.name.primary, gene.name.synonym and organism.name.scientific

Examples

# using internal data
data("protein_json")
prot_names <- extract_names(protein_json)
# generates a list of 6

## Not run: 
# access the Uniprot Protein API
uniprot_acc <- c("Q04206")  # change this for your fav protein
# Get UniProt entry by accession
acc_uniprot_url <-
    c("https://www.ebi.ac.uk/proteins/api/proteins?accession=")
comb_acc_api <- paste0(acc_uniprot_url, uniprot_acc)
# basic function is GET() which accesses the API
# requires internet access
protein <- httr::GET(comb_acc_api, accept_json())
status_code(protein)  # returns a 200 means it worked
# use content() function from httr to give us a list
protein_json <- httr::content(protein) # gives a Large list
# with 14 primary parts and lots of bits inside
# function from my package to extract names of protein
names <- extract_names(protein_json)

## End(Not run)

brennanpincardiff/drawProteins documentation built on March 8, 2024, 8:15 a.m.