Phenotypes: Phenotypes

In SwanseaUniversityMedical/ConceptLibraryClient: Concept Library API Client

Phenotypes

Description

Phenotypes object, inheriting from ConceptLibraryClient::Endpoint - allows querying of phenotypes/ endpoints

Value

Response object

Response object

Response object

Response object

Response object

Response object

Data read in from the file

Formatted phenotype data

Formatted concept data

Formatted concept data

Concept component

Formatted phenotype data

Super class

ConceptLibraryClient::Endpoint -> Phenotypes

Public fields

ALLOWED_FILE_EXTENSIONS

(list) List of file extensions allowed

PHENOTYPE_IGNORE_FILEDS

(list) List of fields to ignore

Active bindings

ALLOWED_FILE_EXTENSIONS

(list) List of file extensions allowed

PHENOTYPE_IGNORE_FILEDS

(list) List of fields to ignore

Methods

Public methods

• Phenotypes$get()

• Phenotypes$get_versions()

• Phenotypes$get_detail()

• Phenotypes$get_codelist()

• Phenotypes$save_definition_file()

• Phenotypes$create()

• Phenotypes$update()

• Phenotypes$clone()

Inherited methods

• ConceptLibraryClient::Endpoint$initialize()

---

Method get()

Queries phenotypes/, with optional query parameters

Usage

Phenotypes$get(...)

Arguments

...

(list) List of optional parameters

---

Method get_versions()

Queries phenotypes/id/get-versions/

Usage

Phenotypes$get_versions(phenotype_id)

Arguments

phenotype_id

(string) Id of entity to query

---

Method get_detail()

Queries phenotypes/id/detail/ or phenotypes/id/version/id/detail/

Usage

Phenotypes$get_detail(phenotype_id, version_id = NA)

Arguments

phenotype_id

(string) Id of entity to query

version_id

(integer) Version id of entity to query

---

Method get_codelist()

Queries phenotypes/id/export/codes/ or phenotypes/id/version/id/export/codes/

Usage

Phenotypes$get_codelist(phenotype_id, version_id = NA)

Arguments

phenotype_id

(string) Id of entity to query

version_id

(integer) Version id of entity to query

---

Method save_definition_file()

Formats phenotype detail and saves it to file

Usage

Phenotypes$save_definition_file(path, phenotype_id, version_id = NA)

Arguments

path

(string) Path to save the file

phenotype_id

(string) Id of entity to query

version_id

(integer) Version id of entity to query

---

Method create()

Creates a new phenotype based on the .yaml file supplied

Usage

Phenotypes$create(path)

Arguments

path

(string) Path to definition file

---

Method update()

Updates an existing phenotype with details from the .yaml file supplied

Usage

Phenotypes$update(path)

Arguments

path

(string) Path to definition file

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Phenotypes$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

SwanseaUniversityMedical/ConceptLibraryClient documentation built on April 14, 2025, 12:45 p.m.