Retrieves PGS publications via the PGS Catalog REST API. The REST
API is queried multiple times with the criteria passed as arguments (see
below). By default all publications that match the criteria supplied in the
arguments are retrieved: this corresponds to the default option
set_operation
set to 'union'
. If you rather have only the
associations that match simultaneously all criteria provided, then set
set_operation
to 'intersection'
.
Usage
get_publications(
pgp_id = NULL,
pgs_id = NULL,
pubmed_id = NULL,
author = NULL,
set_operation = "union",
interactive = TRUE,
verbose = FALSE,
warnings = TRUE,
progress_bar = TRUE
)
Arguments
- pgp_id
A character vector of PGS Catalog publication accession identifiers.
- pgs_id
A
character
vector of PGS Catalog score accession identifiers.- pubmed_id
An
integer
vector of PubMed identifiers.- author
A character vector of author names, any author in the list of authors in a publication, .e.g.
'Mavaddat'
.- set_operation
Either
'union'
or'intersection'
. This tells how publications retrieved by different criteria should be combined:'union'
binds together all results removing duplicates and'intersection'
only keeps same publications found with different criteria.- interactive
A logical. If all publications are requested, whether to ask interactively if we really want to proceed.
- verbose
A
logical
indicating whether the function should be verbose about the different queries or not.- warnings
A
logical
indicating whether to print warnings, if any.- progress_bar
Whether to show a progress bar as the queries are performed.
Value
A publications object.
Details
Please note that all search criteria are vectorised, thus allowing for batch
mode search. For more details see the help vignette:
vignette("getting-pgs-publications", package = "quincunx")
.
Examples
if (FALSE) {
# Get PGS publications by their identifier
get_publications(pgp_id = c('PGP000001', 'PGP000002'))
# By polygenic score identifier
get_publications(pgs_id = 'PGS000003')
# By PubMed identifier
get_publications(pubmed_id = '30554720')
# By author's last name
get_publications(author = 'Natarajan')
}