locate_url_ann: Construct the URL to a recount3 annotation file

In LieberInstitute/recount3: Explore and download data from the recount3 project

Construct the URL to a recount3 annotation file

Description

Given a expression feature type, organism and annotation, this function constructs the URL (or file path) to access a recount3 annotation file. This function is used by create_rse_manual().

Usage

locate_url_ann(
  type = c("gene", "exon"),
  organism = c("human", "mouse"),
  annotation = annotation_options(organism),
  recount3_url = getOption("recount3_url", "http://duffel.rail.bio/recount3")
)

Arguments

type	A character(1) specifying whether you want to access gene counts or exon data.
organism	A character(1) specifying which organism you want to download data from. Supported options are "human" or "mouse".
annotation	A character(1) specifying which annotation you want to download. Only used when type is either gene or exon.
recount3_url	A character(1) specifying the home URL for recount3 or a local directory where you have mirrored recount3. Defaults to the load balancer http://duffel.rail.bio/recount3, but can also be https://recount-opendata.s3.amazonaws.com/recount3/release from https://registry.opendata.aws/recount/ or SciServer datascope from IDIES at JHU https://sciserver.org/public-data/recount3/data. You can set the R option recount3_url (for example in your .Rprofile) if you have a favorite mirror.

Value

A character(1) with the URL (or file path) to access the recount3 annotation file.

See Also

Other internal functions for accessing the recount3 data: annotation_ext(), create_rse_manual(), file_retrieve(), locate_url(), project_homes(), read_counts(), read_metadata()

Examples

locate_url_ann()
locate_url_ann(organism = "mouse")

LieberInstitute/recount3 documentation built on May 10, 2023, 6:01 a.m.