Retrieves polygenic scores via the PGS Catalog REST API. The REST
API is queried multiple times with the criteria passed as arguments (see
below). By default all scores 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_scores(
pgs_id = NULL,
efo_id = NULL,
pubmed_id = NULL,
set_operation = "union",
interactive = TRUE,
verbose = FALSE,
warnings = TRUE,
progress_bar = TRUE
)
Arguments
- pgs_id
A
character
vector of PGS Catalog score accession identifiers.- efo_id
A character vector of EFO identifiers.
- pubmed_id
An
integer
vector of PubMed identifiers.- set_operation
Either
'union'
or'intersection'
. This tells how scores retrieved by different criteria should be combined:'union'
binds together all results removing duplicates and'intersection'
only keeps same scores found with different criteria.- interactive
A logical. If all scores 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 scores object.