Function reference • quincunx

Get PGS Catalog Data

Receive data from the PGS Catalog REST API.

get_scores(): Get PGS Catalog Scores

read_scoring_file(): Read a polygenic scoring file

get_publications(): Get PGS Catalog Publications

get_performance_metrics(): Get PGS Catalog Performance Metrics

get_sample_sets(): Get PGS Catalog Sample Sets

get_traits(): Get PGS Catalog Traits

get_cohorts(): Get PGS Catalog Cohorts

get_trait_categories(): Get PGS Catalog Trait Categories

get_ancestry_categories(): Get ancestry categories and classes

get_releases(): Get PGS Catalog Releases

PGS Catalog Entities

S4 classes for scores, publications, performance_metrics, sample_sets and traits.

scores-class: An S4 class to represent a set of PGS Catalog Polygenic Scores

publications-class: An S4 class to represent a set of PGS Catalog Publications

performance_metrics-class: An S4 class to represent a set of PGS Catalog Performance Metrics

sample_sets-class: An S4 class to represent a set of PGS Catalog Sample Sets

traits-class: An S4 class to represent a set of PGS Catalog Traits

Other Entities

S4 classes for cohorts, trait_categories and releases.

cohorts-class: An S4 class to represent a set of cohorts

trait_categories-class: An S4 class to represent a set of PGS Catalog Trait Categories

releases-class: An S4 class to represent a set of PGS Catalog Releases

Data Wrangling of PGS Catalog Entities

S4 methods for combining and tallying scores, publications, performance_metrics, sample_set, traits, cohorts, trait_categories and releases.

n(): Number of PGS Catalog entities

bind(): Bind PGS Catalog objects

union() intersect() setdiff() setequal(): Set operations on PGS Catalog objects

Accession identifier mapping

Translate accession identifiers between scores, publications, performance_metrics, sample_set, traits and GWAS studies.

pgs_to_pgp(): Map PGS identifiers to PGP identifiers

pgs_to_pss(): Map PGS identifiers to PSS identifiers

pgs_to_ppm(): Map PGS identifiers to PPM identifiers

pgs_to_study(): Map PGS identifiers to GWAS study identifiers

study_to_pgs(): Map GWAS studies identifiers to PGS identifiers

pgp_to_pgs(): Map PGP identifiers to PGS identifiers

pgp_to_pss(): Map PGP identifiers to PSS identifiers

pgp_to_ppm(): Map PGP identifiers to PPM identifiers

pss_to_pgs(): Map PSS identifiers to PGS identifiers

pss_to_pgp(): Map PSS identifiers to PGP identifiers

pss_to_ppm(): Map PSS identifiers to PPM identifiers

ppm_to_pgs(): Map PPM identifiers to PGS identifiers

ppm_to_pgp(): Map PPM identifiers to PGP identifiers

ppm_to_pss(): Map PPM identifiers to PSS identifiers

Easily navigate web resources

Functions that allow you to quickly browse linked information.

open_in_pgs_catalog(): Browse PGS Catalog entities from the PGS Catalog Web Graphical User Interface

open_in_pubmed(): Browse PubMed from PubMed identifiers.

open_in_dbsnp(): Browse dbSNP from SNP identifiers.

Export to xlsx

Exporting scores, publications, performance_metrics, sample_set, traits, cohorts, trait_categories and releases to xlsx.

write_xlsx(): Export a PGS Catalog object to xlsx

Miscellaneous

Other functions.

clear_cache(): Clear quincunx cache of memoised functions

Datasets

Datasets shipped with quincunx

stages: Study stages

ancestry_categories: Ancestry categories and classes