getAnnotationHubOption: Get and set options for default AnnotationHub behavior.

Description Usage Arguments Details Value Author(s) Examples

View source: R/AnnotationHubOption.R

Description

These functions get or set options for creation of new ‘AnnotationHub’ instances.

Usage

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Arguments

arg

The character(1) hub options to set. see ‘Details’ for current options.

value

The value to be assigned to the hub option.

Details

Supported options include:

“URL”:

character(1). The base URL of the annotation hub. Default: https://annotationhub.bioconductor.org

“CACHE”:

character(1). The location of the hub cache. Default: “AnnotationHub” in the user's directory established by rappdirs::user_cache_dir().

“MAX_DOWNLOADS”:

numeric(1). The integer number of downloads allowed before triggering an error. This is to help avoid accidental download of a large number of AnnotationHub members.

“PROXY”:

request object returned by httr::use_proxy(). The request object describes a proxy connection allowing Internet access, usually through a restrictive firewall. Setting this option sends all AnnotationHub requests through the proxy. Default: NULL.

In setHubOption("PROXY", value), value can be one of NULL, a request object returned by httr::use_proxy(), or a well-formed URL as character(1). The URL can be completely specified by http://username:[email protected]:8080; username:password and port (e.g. :8080) are optional.

“TESTING”:

logical(1). TRUE/FALSE should the AnnotationHub testing environment be used. AnnotationHub does automatic filtering particularly with regards to OrgDbs. The TESTING=TRUE setting will allow for all OrgDbs for a given devel version to also be displayed. (This option should really only be set by a OrgDb contributing maintainer for testing and debugging). Default: FALSE.

“LOCAL”:

logical(1). TRUE/FALSE should the AnnotationHub create a hub consisting only of previously downloaded resourcesd. Default: FALSE.

“ASK”:

logical(1). TRUE/FALSE should the AnnotationHub ask if the hub location should be created. If FALSE, the default location will be used and created if it doesn't exist without asking. If TRUE will ask the user and if in a non interactive session utilize a temporary directoy for the caching. Default: TRUE.

Default values may also be determined by system and global R environment variables visible before the package is loaded. Use options or variables preceeded by “ANNOTATION_HUB_”, e.g., options(ANNOTATION_HUB_MAX_DOWNLOADS=10) prior to package load sets the default number of downloads to 10.

Value

The requested or successfully set option.

Author(s)

Martin Morgan [email protected] and Lori Shepherd

Examples

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getAnnotationHubOption("URL")
## Not run: 
setAnnotationHubOption("CACHE", "~/.myHub")

## End(Not run)

Bioconductor/AnnotationHub documentation built on Dec. 2, 2019, 10:48 p.m.