ancestry_categories: Ancestry categories and classes

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

Ancestry categories and classes

Description

A dataset containing the ancestry categories defined in NHGRI-EBI GWAS Catalog framework (Table 1, doi: 10.1186/s13059-018-1396-2). Ancestry categories are assigned to samples with distinct and well-defined patterns of genetic variation. You will find these categories in the variable ancestry_category of the following objects: scores, performance_metrics and sample_sets. Ancestry categories (ancestry_category) are further clustered into ancestry classes (ancestry_class).

Usage

ancestry_categories

Format

A data frame with 19 ancestry categories (rows) and 6 columns:

ancestry_category

Ancestry category.

ancestry_class

To reduce the complexity associated with the many ancestry categories, some have been merged into higher-level groupings (ancestry_class). These groupings represent the current breadth of data in the PGS Catalog and are likely to change as more data is added.

ancestry_class_symbol

3-letter code for the ancestry_class e.g. "EUR" or "MAE".

ancestry_class_colour

Hexadecimal colour code associated with ancestry groupings (ancestry_class). This can be useful when visually communicating about ancestries.

definition

Description of the ancestry category.

examples

Examples of detailed descriptions of sample ancestries included in the category.

Source

Table 1 of Moralles et al. (2018):

doi: 10.1186/s13059-018-1396-2

PGS Catalog Ancestry Documentation:

http://www.pgscatalog.org/docs/ancestry/

Examples

ancestry_categories

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