BioMartClient: BioMart API Client

In bhklab/AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data

BioMart API Client

Description

Client class for interacting with the BioMart REST API.

Details

This class provides methods for querying BioMart REST API endpoints, retrieving information about available marts, datasets, attributes, and filters.

Public fields

base_url

Base URL of the BioMart service

path

Path to the BioMart API on the server

Methods

Public methods

• BioMartClient$new()

• BioMartClient$get_marts()

• BioMartClient$get_datasets()

• BioMartClient$get_attributes()

• BioMartClient$get_filters()

• BioMartClient$clone()

---

Method new()

Initialize a new BioMartClient

Usage

BioMartClient$new(base_url, path = "/biomart")

Arguments

base_url

Character, the base URL of the BioMart service

path

Character, the API path, defaults to "/biomart"

Returns

A new BioMartClient object

---

Method get_marts()

Retrieve available marts from the BioMart service

Usage

BioMartClient$get_marts()

Returns

List of MartInfo objects

---

Method get_datasets()

Retrieve available datasets for a given mart

Usage

BioMartClient$get_datasets(mart)

Arguments

mart

MartInfo object, the mart to query

Returns

List of DatasetInfo objects

---

Method get_attributes()

Retrieve available attributes for a given dataset

Usage

BioMartClient$get_attributes(dataset)

Arguments

dataset

DatasetInfo object, the dataset to query

Returns

List of attribute information

---

Method get_filters()

Retrieve available filters for a given dataset

Usage

BioMartClient$get_filters(dataset)

Arguments

dataset

DatasetInfo object, the dataset to query

Returns

List of filter information

---

Method clone()

The objects of this class are cloneable with this method.

Usage

BioMartClient$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## Not run: 
# Create a client for Ensembl BioMart
client <- BioMartClient$new("https://www.ensembl.org")

# Get available marts
marts <- client$get_marts()

# Select a mart and get its datasets
ensembl <- marts[[1]]
datasets <- client$get_datasets(ensembl)

## End(Not run)

bhklab/AnnotationGx documentation built on April 3, 2025, 4:27 p.m.