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

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Cohorts

A cohort is a group of individuals with a shared characteristic. Cohorts are identified in quincunx by the cohort_symbol variable. Participants in cohorts are used to define samples, which in turn, are used to assemble sample sets. For more details on the relationship between the concepts of cohorts, samples and sample sets, see vignette('cohorts-samples-sample-sets').

Given that study participants typically come from one or more catalogued cohorts and that cohorts can have a strong bias ancestry composition --- i.e., most cohorts are mostly composed of European-ancestry individuals ---, it can be really important to know which cohorts have been used at the different stages of a Polygenic Score (PGS) life cycle to assess the transferability of PGS performance [@reisberg2017;@martin2019;@duncan2019].

Getting cohorts

If you know beforehand the cohort acronyms (e.g., "23andMe") that you are interested in, then you can get their full name and associated PGS identifiers using the get_cohorts() function by providing their symbols with the parameter cohort_symbol:

library(quincunx)
get_cohorts(cohort_symbol = '23andMe')

The pgs_ids slot contains a tibble of associated PGS identifiers with the queried cohorts. The stage variable indicates the PGS stage in which the cohort was used.

To get all catalogued cohorts in the PGS Catalog, leave the cohort_symbol parameter as NULL (default). Note that, in this case, it may take a few minutes for the download to complete.

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maialab/quincunx documentation built on Aug. 18, 2022, 5:31 a.m.