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().
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")
)A character(1) specifying whether you want to access gene
counts or exon data.
A character(1) specifying which organism you want to
download data from. Supported options are "human" or "mouse".
A character(1) specifying which annotation you want to
download. Only used when type is either gene or exon.
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.
A character(1) with the URL (or file path) to access the
recount3 annotation file.
Other internal functions for accessing the recount3 data:
annotation_ext(),
create_rse_manual(),
file_retrieve(),
locate_url(),
project_homes(),
read_counts(),
read_metadata()
locate_url_ann()
#> human.gene_sums.G026.gtf.gz
#> "http://duffel.rail.bio/recount3/human/annotations/gene_sums/human.gene_sums.G026.gtf.gz"
locate_url_ann(organism = "mouse")
#> mouse.gene_sums.M023.gtf.gz
#> "http://duffel.rail.bio/recount3/mouse/annotations/gene_sums/mouse.gene_sums.M023.gtf.gz"