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

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

Cohorts

A cohort is a group of individuals with a shared characteristic. Cohorts are identified in quincunx by the cohort_symbol variable. See vignette('getting-cohorts') on how to find associated polygenic scores.

knitr::include_graphics('../man/figures/cohorts.svg')

Using get_cohorts() to retrieve associated PGS identifiers with cohort "PROMIS":

get_cohorts('PROMIS')

Samples

A sample is a group of participants associated with none, one or more catalogued cohorts. The selection from a cohort can be either a subset or its totality. Samples are not identified in PGS Catalog with a global unique identifier, but quincunx assigns a surrogate identifier (sample_id) to allow relations between tables.

knitr::include_graphics('../man/figures/samples.svg')

Sample composition is provided in slot cohorts from objects scores returned by the get_scores() function.

library(dplyr, warn.conflicts = FALSE)

# PGS000011 is one of the polygenic scores that is based upon participants from
# cohort PROMIS
pgs_11 <- get_scores('PGS000011')

# Cohort PROMIS is included in sample no. 2, along with LOLIPOP
filter(pgs_11@cohorts, sample_id == 2L)

To know a few more details about samples, look into the samples slot of the object scores:

filter(pgs_11@samples, sample_id == 2L)

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).

knitr::include_graphics('../man/figures/sample_sets.svg')

To find the sample sets that included a specific cohort, we start by getting the PGS identifiers associated with a cohort, e.g. MHI:

# Note that by the definition of sample set, samples included in sample sets
# are only used at PGS evaluation stages.
filter(get_cohorts('MHI')@pgs_ids, stage == 'eval')

PGS000013 is one of the polygenic scores whose evaluation used participants from the cohort MHI. We retrieve now the sample sets used in the evaluation of PGS000013:

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

One of the sample sets used to evaluate PGS000013 is PSS000020. We can retrieve a sample_set object that contains its composition, i.e., the samples and cohorts included, along with other details: