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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(quincunx)

Sample sets

A sample set is a group of samples used in a polygenic score evaluation.Each sample set is identified in the PGS Catalog by a unique sample set identifier (pss_id). See vignette('cohorts-samples-sample-sets') for more details on the relationship between cohorts, samples, and sample sets.

Getting sample sets

To get information on sample sets you can either search by the associated polygenic score identifiers, or by the sample set identifiers themselves (if you know them beforehand).

By the PGS identifier

# Sample sets used in the evaluation of the PGS000013
(pgs_13_sset <- get_sample_sets(pgs_id = 'PGS000013'))

By the sample set identifier

# Sample set PSS000020
(pss_20 <- get_sample_sets(pss_id = 'PSS000020'))

By trait or disease

If you wish to search by other criteria other than the PGS identifier or the PSS identifier, then you will need to do it in several steps. The general approach is to map your criteria to matching PGS identifiers and from those PGS IDs to sample sets using get_sample_sets().

Let's say that you want to retrieve all sample sets used in the evaluation of polygenic scores for the disease Vitiligo (loss of skin melanocytes that causes areas of skin depigmentation).

knitr::include_graphics('../man/figures/vitiligo.png') 

We start by searching for this disease in the PGS Catalog with get_traits():

(traits_vitiligo <- get_traits(trait_term = 'Vitiligo'))

The slot pgs_ids contains the polygenic score identifiers associated with Vitiligo.

traits_vitiligo@pgs_ids

Now to search for the sample sets, we can pass those PGS identifiers to get_sample_sets():

(pss_vitiligo <- get_sample_sets(pgs_id = traits_vitiligo@pgs_ids$pgs_id))

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