traits-class: An S4 class to represent a set of PGS Catalog Traits

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

An S4 class to represent a set of PGS Catalog Traits

Description

The traits object consists of six slots, each a table (tibble), that combined form a relational database of a subset of PGS Catalog traits. Each trait is an observation (row) in the traits table — main table. All tables have the column efo_id as primary key.

Slots

traits

A table of traits. Columns:

efo_id

An EFO identifier.

parent_efo_id

An EFO identifier of the parent trait.

is_child

Is this trait obtained because it is a child of other trait?

trait

Trait name.

description

Detailed description of the trait from EFO.

url

External link to the EFO entry.

pgs_ids

A table of associated polygenic score identifiers. Columns:

efo_id

An EFO identifier.

parent_efo_id

An EFO identifier of the parent trait.

is_child

Is this trait obtained because it is a child of other trait?

pgs_id

Polygenic Score (PGS) identifier.

child_pgs_ids

A table of polygenic score identifiers associated with the child traits. Columns:

efo_id

An EFO identifier.

parent_efo_id

An EFO identifier of the parent trait.

is_child

Is this trait obtained because it is a child of other trait?

child_pgs_id

Polygenic Score (PGS) identifiers associated with child traits.

trait_categories

A table of associated trait categories. Columns:

efo_id

An EFO identifier.

parent_efo_id

An EFO identifier of the parent trait.

is_child

Is this trait obtained because it is a child of other trait?

trait_category

Trait category name.

trait_synonyms

A table of associated trait synonyms. Columns:

efo_id

An EFO identifier.

parent_efo_id

An EFO identifier of the parent trait.

is_child

Is this trait obtained because it is a child of other trait?

trait_synonyms

Trait synonyms.

trait_mapped_terms

A table of associated external references, identifiers or other terms. Columns:

efo_id

An EFO identifier.

parent_efo_id

An EFO identifier of the parent trait.

is_child

Is this trait obtained because it is a child of other trait?

trait_mapped_terms

Trait mapped terms.

quincunx documentation built on July 9, 2023, 7:32 p.m.