In maialab/quincunx: REST API Client for the 'PGS' Catalog

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

PGS Publications

PGS publications are those published works that underlie the data provided by the PGS Catalog.

To retrieve these publications use the function get_publications(). You may use one of the following search criteria (or a combination thereof):

pgp_id: the publication identifier assigned by the PGS Catalog;
pgs_id: the polygenic score identifier;
pubmed_id: PubMed identifier;
author: an author last name.

If you do not pass any of the criteria above, then get_publications() will retrieve all publications in the Catalog.

Getting PGS Publications

Getting PGS publications by their identifiers:

library(quincunx)

get_publications(pgp_id = c('PGP000001', 'PGP000002'))

By pgs_id:

library(quincunx)

get_publications(pgs_id = 'PGS000003')

By pubmed_id:

library(quincunx)

get_publications(pubmed_id = '30554720')

By author:

library(quincunx)

get_publications(author = 'Natarajan')

Getting PGS Publications by other criteria

The PGS Catalog REST API only supports searches by those criteria mentioned above. If you would like to get results by other criteria, e.g., publication_date, then you need to retrieve all publications and filter them afterwards.

As an example, let's download all publications and then keep only those publications published in 2021:

all_pub <- get_publications(interactive = FALSE)
all_pub@publications

Filtering based on the year 2021:

library(dplyr, warn.conflicts = FALSE)

# Determine the PGP ids whose publication date falls within 2021.
pgp_ids_2021 <-
  filter(
    all_pub@publications,
    publication_date >= '2021-01-01' &
      publication_date <= '2021-12-31'
  ) %>%
  pull('pgp_id')

# Filtering based on the PGP ids
pub_2021 <- all_pub[pgp_ids_2021]

# Print the first 10 PGS publications
pub_2021@publications