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 performance1–3.
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')
#> An object of class "cohorts"
#> Slot "cohorts":
#> # A tibble: 1 × 2
#> cohort_symbol cohort_name
#> <chr> <chr>
#> 1 23andMe 23andMe
#>
#> Slot "pgs_ids":
#> # A tibble: 31 × 3
#> cohort_symbol pgs_id stage
#> <chr> <chr> <chr>
#> 1 23andMe PGS000079 gwas/dev
#> 2 23andMe PGS000157 gwas/dev
#> 3 23andMe PGS000336 gwas/dev
#> 4 23andMe PGS000730 gwas/dev
#> 5 23andMe PGS000731 gwas/dev
#> 6 23andMe PGS000732 gwas/dev
#> 7 23andMe PGS000766 gwas/dev
#> 8 23andMe PGS000767 gwas/dev
#> 9 23andMe PGS000780 gwas/dev
#> 10 23andMe PGS000790 gwas/dev
#> # ℹ 21 more rowsThe 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.