Get and set options for default AnnotationHub behavior.

Description

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

Usage

getAnnotationHubOption(arg)
setAnnotationHubOption(arg, value)

Arguments

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 home directory.

“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:password@proxy.dom.com:8080; username:password and port (e.g. :8080) are optional.

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 mtmorgan@fhcrc.org

Examples

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

## End(Not run)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(AnnotationHub)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/AnnotationHub/getAnnotationHubOption.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getAnnotationHubOption
> ### Title: Get and set options for default AnnotationHub behavior.
> ### Aliases: getAnnotationHubOption setAnnotationHubOption
> ### Keywords: manip
> 
> ### ** Examples
> 
> getAnnotationHubOption("URL")
[1] "https://annotationhub.bioconductor.org"
> ## Not run: 
> ##D setAnnotationHubOption("CACHE", "~/.myHub")
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>