locate_url_ann {recount3}

R Documentation

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.

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")

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