MgnifyClient: Constructor for creating a MgnifyClient object to allow the...

In beadyallen/MGnifyR: R interface to EBI MGnify metagenomics resource

Constructor for creating a MgnifyClient object to allow the access to MGnify database.

Description

Constructor for creating a MgnifyClient object to allow the access to MGnify database.

A MgnifyClient object

Usage

MgnifyClient(
  username = NULL,
  password = NULL,
  useCache = FALSE,
  cacheDir = tempdir(),
  showWarnings = FALSE,
  verbose = TRUE,
  clearCache = FALSE,
  ...
)

Arguments

username	A single character value specifying an optional username for authentication. (By default: username = NULL)
password	A single character value specifying an optional password for authentication. (By default: password = NULL)
useCache	A single boolean value specifying whether to enable on-disk caching of results during this session. In most use cases should be TRUE. (By default: useCache = FALSE)
cacheDir	A single character value specifying a folder to contain the local cache. Note that cached files are persistent, so the cache directory may be reused between sessions, taking advantage of previously downloaded results. The directory will be created if it doesn't exist already. (By default: cacheDir = tempdir())
showWarnings	A single boolean value specifying whether to print warnings during invocation of some MGnifyR functions. (By default: showWarnings = FALSE)
verbose	A single boolean value specifying whether to print extra output during invocation of some MGnifyR functions. (By default: verbose = FALSE)
clearCache	A single boolean value specifying whether to clear the cache. (By default: clearCache = FALSE)
...	optional arguments: url A single character value specifying an url address of the database. (By default: url = "https://www.ebi.ac.uk/metagenomics/api/v1")

Details

All functions in the MGnifyR package take a MgnifyClient object as their first argument. While not essential to querying the raw MGnify API (which is exposed as relative standard JSONAPI), the object allows the simple handling of both user authentication and access to private data, and local on-disk caching of results.

An object that are required by functions of MGnifyR package.

Value

A MgnifyClient object.

Slots

databaseUrl

A single character value specifying an URL address of database.

authTok

A single character value specifying authentication token.

useCache

A single boolean value specifying whether to use cache.

cacheDir

A single character value specifying cache directory.

showWarnings

A single boolean value specifying whether to show warnings.

clearCache

A single boolean value specifying whether to clear cache.

verbose

A single boolean value specifying whether to show messages.

Constructor

See MgnifyClient for constructor.

Accessor

See MgnifyClient-accessors for accessor functions.

Examples

my_client <- MgnifyClient(
    useCache = TRUE, cacheDir = "/scratch/MGnify_cache_location"
    )

## Not run: 
# Use username and password to get access to non-public data
my_client <- MgnifyClient(
    username = "Webin-1122334", password = "SecretPassword",
    useCache = TRUE, cacheDir = "/scratch/MGnify_cache_location"
    )

## End(Not run)

beadyallen/MGnifyR documentation built on March 30, 2024, 4:48 a.m.